Polypeptides having endoglucanase activity and polynucleotides encoding same

ABSTRACT

The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.12/294,506 filed on Sep. 25, 2008, which is a 35 U.S.C. 371 nationalapplication of PCT/US07/65639 filed on Mar. 30, 2007 and claims priorityfrom U.S. provisional application Ser. No. 60/788,523 filed on Mar. 30,2006, which applications are fully incorporated herein by reference.

REFERENCE TO A DEPOSIT OF BIOLOGICAL MATERIAL

This application contains a reference to deposits of biological materialwhich have been made at the Northern Regional Research Center (NRRL)under the Budapest Treaty and assigned accession numbers NRRLB-30898 andNRRLB-30901, which microbial deposits are incorporated herein byreference.

REFERENCE TO A SEQUENCE LISTING

This application contains a Sequence Listing in computer readable form.The computer readable form is incorporated herein by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to isolated polypeptides havingendoglucanase activity and isolated polynucleotides encoding thepolypeptides. The invention also relates to nucleic acid constructs,vectors, and host cells comprising the polynucleotides as well asmethods for producing and using the polypeptides.

2. Description of the Related Art

Cellulose is a polymer of the simple sugar glucose covalently bonded bybeta-1,4-linkages. Many microorganisms produce enzymes that hydrolyzebeta-linked glucans. These enzymes include endoglucanases,cellobiohydrolases, and beta-glucosidases. Endoglucanases digest thecellulose polymer at random locations, opening it to attack bycellobiohydrolases. Celiobiohydrolases sequentially release molecules ofcellobiose from the ends of the cellulose polymer. Cellobiohydrolase Iis a 1,4-beta-D-glucan cellobiohydrolase (E.C. 3.2.1.91) activity thatcatalyzes the hydrolysis of 1,4-beta-D-glucosidic linkages in cellulose,cellotetriose, or any beta-1,4-linked glucose containing polymer,releasing cellobiose from the reducing ends of the chain.Cellobiohydrolase II is a 1,4-beta-D-glucan cellobiohydrolase (E.C.3.2.1.91) activity that catalyzes the hydrolysis of1,4-beta-D-glucosidic linkages in cellulose, cellotetriose, or anybeta-1,4-linked glucose containing polymer, releasing cellobiose fromthe non-reducing ends of the chain. Cellobiose is a water-solublebeta-1,4-linked dimer of glucose. Beta-glucosidases hydrolyze cellobioseto glucose.

The conversion of cellulosic feedstocks into ethanol has the advantagesof the ready availability of large amounts of feedstock, thedesirability of avoiding burning or land filling the materials, and thecleanliness of the ethanol fuel. Wood, agricultural residues, herbaceouscrops, and municipal solid wastes have been considered as feedstocks forethanol production. These materials primarily consist of cellulose,hemicellulose, and lignin. Once the cellulose is converted to glucose,the glucose is easily fermented by yeast into ethanol.

Kvesitadaze at al., 1995, Applied Biochemistry and Biotechnology 50:137-143, describe the isolation and properties of a thermostableendoglucanase from a thermophilic mutant strain of Thielavia terrestris.Gilbert et al., 1992, Bioresource Technology 39: 147-154, describe thecharacterization of the enzymes present in the cellulose system ofThielavia terrestris 255B. Breuil at al., 1986, Biotechnology Letters 8:673-676, describe production and localization of cellulases andbeta-glucosidases from Thielavia terrestris strains C464 and NRRL 8126.

It would be an advantage in the art to identify new endoglucanaseshaving improved properties, such as improved hydrolysis rate, betterthermal stability, reduced adsorption to lignin, and ability tohydrolyze non-cellulosic components of biomass, such as hemicellulose,in addition to hydrolyzing cellulose. Endoglucanases with a broad rangeof side activities on hemicellulose can be especially beneficial forimproving the overall hydrolysis yield of complex, hemicellulose-richbiomass substrates.

It is an object of the present invention to provide improvedpolypeptides having endoglucanase activity and polynucleotides encodingthe polypeptides.

SUMMARY OF THE INVENTION

The present invention relates to isolated polypeptides havingendoglucanase activity selected from the group consisting of:

(a) a polypeptide comprising an amino acid sequence having at least 90%identity with the mature polypeptide of SEQ ID NO: 2 or at least 60%identity with the mature polypeptide of SEQ ID NO: 4;

(b) a polypeptide which is encoded by a polynucleotide which hybridizesunder at least high stringency conditions with (i) the maturepolypeptide coding sequence of SEQ ID NO: 1, (ii) the cDNA sequencecontained in the mature polypeptide coding sequence of SEQ ID NO: 1, or(iii) a complementary strand of (1) or (ii), or under at least mediumstringency conditions with (i) the mature polypeptide coding sequence ofSEQ ID NO: 3, (ii) the genomic DNA sequence comprising the maturepolypeptide coding sequence of SEQ ID NO: 3, or (iii) a complementarystrand of (i) or (ii);

(c) a polypeptide which is encoded by a polynucleotide comprising anucleotide sequence having at least 90% identity with the maturepolypeptide coding sequence of SEQ ID NO: 1 or at least 60% identitywith the mature polypeptide coding sequence of SEQ ID NO: 3; and

(d) a variant comprising a substitution, deletion, and/or insertion ofone or more amino acids of the mature polypeptide of SEQ ID NO: 2 or SEQID NO: 4.

The present invention also relates to isolated polynucleotides encodingpolypeptides having endoglucanase activity, selected from the groupconsisting of:

(a) a polynucleotide encoding a polypeptide comprising an amino acidsequence having at least 90% identity with the mature polypeptide of SEQID NO: 2 or at least 60% identity with the mature polypeptide of SEQ IDNO: 4;

(b) a polynucleotide which hybridizes under at least high stringencyconditions with (i) the mature polypeptide coding sequence of SEQ ID NO:1, (ii) the cDNA sequence contained in the mature polypeptide codingsequence of SEQ ID NO: 1, or (iii) a complementary strand of (i) or(ii), or under at least medium stringency conditions with (i) the maturepolypeptide coding sequence of SEQ ID NO: 3, (ii) the genomic DNAsequence comprising the mature polypeptide coding sequence of SEQ ID NO:3, or (iii) a complementary strand of (i) flr (ii):

(c) a polynucleotide comprising a nucleotide sequence having at least90% identity with the mature polypeptide coding sequence of SEQ ID NO: 1or at least 60% identity with the mature polypeptide coding sequence ofSEQ ID NO: 3; and

(d) a polynucleotide encoding a variant comprising a substitution,deletion, and/or insertion of one or more amino acids of the maturepolypeptide of SEQ ID NO: 2 or SEQ ID NO: 4.

In a preferred aspect, the mature polypeptide is amino acids 19 to 396of SEQ ID NO: 2. In another preferred aspect, the mature polypeptide isamino acids 20 to 400 of SEQ ID NO: 4. In another preferred aspect, themature polypeptide coding sequence is nucleotides 110 to 1557 of SEQ IDNO: 1. In another preferred aspect, the mature polypeptide codingsequence is nucleotides 58 to 1200 of SEQ ID NO: 3.

The present invention also relates to nucleic acid constructs,recombinant expression vectors, recombinant host cells comprising thepolynucleotides, and methods of producing a polypeptide havingendoglucanase activity.

The present invention also relates to methods of inhibiting theexpression of a polypeptide in a cell, comprising administering to thecell or expressing in the cell a double-stranded RNA (dsRNA) molecule,wherein the dsRNA comprises a subsequence of a polynucleotide of thepresent invention. The present also relates to such a double-strandedinhibitory RNA (dsRNA) molecule, wherein optionally the dsRNA is ansiRNA or an miRNA molecule.

The present invention also relates to methods of using the polypeptideshaving endoglucanase activity in the conversion of cellulose to glucoseand various substances.

The present invention also relates to plants comprising an isolatedpolynucleotide encoding such a polypeptide having endoglucanaseactivity.

The present invention also relates to methods for producing such apolypeptide having endoglucanase activity, comprising: (a) cultivating atransgenic plant or a plant cell comprising a polynucleotide encodingsuch a polypeptide having endoglucanase activity under conditionsconducive for production of the polypeptide; and (b) recovering thepolypeptide.

The present invention further relates to nucleic acid constructscomprising a gene encoding a protein, wherein the gene is operablylinked to a nucleotide sequence encoding a signal peptide comprising orconsisting of amino acids 1 to 18 of SEQ ID NO: 2 or amino acids 1 to 19of SEQ ID NO: 4, wherein the gene is foreign to the first and secondnucleotide sequences

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows a restriction map of pPH23.

FIGS. 2A and 2B show the genomic DNA sequence and the deduced amino acidsequence of a Thielavia terrestris NRRL 8126 CEL6B endoglucanase (SEQ IDNOs: 1 and 2, respectively).

FIG. 3 shows a restriction map of pCIBG146.

FIGS. 4A and 4B show the cDNA sequence and the deduced amino acidsequence of a Thielavia terrestris NRRL 8126 CEL6C endoglucanase (SEQ IDNOs: 3 and 4, respectively).

FIG. 5 shows a restriction map of pAlLo1.

FIG. 6 shows a restriction map of pBANe10.

FIG. 7 shows a restriction map of pAlLo2.

FIG. 8 shows a restriction map of pEJG105.

FIG. 9 shows a restriction map of pA2BG146.

DEFINITIONS

Endoglucanase activity: The term “endoglucanase activity” is definedherein as an endo-1,4-beta-D-glucan 4-glucanohydrolase (E.C. No.3.2.1.4) that catalyses the endohydrolysis of 1,4-beta-D-glycosidiclinkages in cellulose, cellulose derivatives (such as carboxymethylcellulose and hydroxyethyl cellulose), lignocellulose, lignocellulosederivatives, lichenin, beta-1,4 bonds in mixed beta-1,3 glucans such ascereal beta-D-glucans or xyloglucans, and other plant materialcontaining cellulosic components. For purposes of the present invention,endoglucanase activity is determined using carboxymethyl cellulose (CMC)hydrolysis according to the procedure of Ghose, 1987, Pure and Appl.Chem. 59: 257-268. One unit of endoglucanase activity is defined as 1.0μmole of reducing sugars produced per minute at 50° C., pH 5.0.

In a preferred aspect, the polypeptides of the present invention havingendogiucanase activity further have enzyme activity toward one or moresubstrates selected from the group consisting of xylan, xyloglucan,arabinoxylan, 1,4-beta-D-mannan, and galactomannan. The activity of thepolypeptides having endoglucanase activity on these polysaccharidesubstrates is determined as percent of the substrate hydrolyzed toreducing sugars after incubating the substrate (5 mg per ml) with apolypeptide having endoglucanase activity of the present invention (5 mgprotein per g of substrate) for 24 hours with intermittent stirring atpH 5.0 (50 mM sodium acetate) and 50° C. Reducing sugars in hydrolysismixtures are determined by the p-hydroxybenzoic acid hydrazide (PHBAH)assay.

In a more preferred aspect, the polypeptides of the present inventionhaving endoglucanase activity further have enzyme activity toward xylan.In another more preferred aspect, the polypeptides of the presentinvention having endoglucanase activity further have enzyme activitytoward xyloglucan. In another more preferred aspect, the polypeptides ofthe present invention having endoglucanase activity further have enzymeactivity toward arabinoxylan. In another more preferred aspect, thepolypeptides of the present invention having endoglucanase activityfurther have enzyme activity toward 1,4-beta-D-mannan. In another morepreferred aspect, the polypeptides of the present invention havingendoglucanase activity further have enzyme activity towardgalactomannan. In another more preferred aspect, the polypeptides of thepresent invention having endoglucanase activity further have enzymeactivity toward xylan, xyloglucan, arabinoxylan, 1,4-beta-D-mannan,and/or galactomannan.

The polypeptides of the present invention have at least 20%, preferablyat least 40%, more preferably at least 50%, more preferably at least60%, more preferably at least 70%, more preferably at least 80%, evenmore preferably at least 90%, most preferably at least 95%, and evenmost preferably at least 100% of the endoglucanase activity of maturepolypeptide of SEQ ID NO: 2 or SEQ ID NO: 4.

Family 6 glycoside hydrolase or Family GH6: The term “Family 6 glycosidehydrolase” or “Family GH6” is defined herein as a polypeptide fallinginto the glycoside hydrolase Family 6 according to Henrissat B., 1991, Aclassification of glycosyl hydrolases based on amino-acid sequencesimilarities, Biochem. J. 280: 309-316, and Henrissat B., and BairochA., 1996, Updating the sequence-based classification of glycosylhydrolases, Biochem. J. 316: 695-696.

Isolated polypeptide: The term “isolated polypeptide” as used hereinrefers to a polypeptide which is at least 20% pure, preferably at least40% pure, more preferably at least 60% pure, even more preferably atleast 80% pure, most preferably at least 90% pure, and even mostpreferably at least 95% pure, as determined by SDS-PAGE.

Substantially pure polypeptide: The term “substantially purepolypeptide” denotes herein a polypeptide preparation which contains atmost 10%, preferably at most 8%, more preferably at most 6%, morepreferably at most 5%, more preferably at most 4%, more preferably atmost 3%, even more preferably at most 2%, most preferably at most 1%,and even most preferably at most 0.5% by weight of other polypeptidematerial with which it is natively or recombinantly associated. It is,therefore, preferred that the substantially pure polypeptide is at least92% pure, preferably at least 94% pure, more preferably at least 95%pure, more preferably at least 96% pure, more preferably at least 96%pure, more preferably at least 97% pure, more preferably at least 98%pure, even more preferably at least 99%, most preferably at least 99.5%pure, and even most preferably 100% pure by weight of the totalpolypeptide material present in the preparation.

The polypeptides of the present invention are preferably in asubstantially pure form. In particular, it is preferred that thepolypeptides are in “essentially pure form”, i.e., that the polypeptidepreparation is essentially free of other polypeptide material with whichit is natively or recombinantly associated. This can be accomplished,for example, by preparing the polypeptide by means of well-knownrecombinant methods or by classical purification methods.

Herein, the term “substantially pure polypeptide” is synonymous with theterms “isolated polypeptide” and “polypeptide in isolated form.”

Mature polypeptide: The term “mature polypeptide” is defined herein as apolypeptide having endoglucanase activity that is in its final formfollowing translation and any post-translational modifications, such asN-terminal processing, C-terminal truncation, glycosylation, etc.

Mature polypeptide coding sequence: The term “mature polypeptide codingsequence” is defined herein as a nucleotide sequence that encodes amature polypeptide having endoglucanase activity.

Identity: The relatedness between two amino acid sequences or betweentwo nucleotide sequences is described by the parameter “identity”.

For purposes of the present invention, the degree of identity betweentwo amino acid sequences is determined using the Needleman-Wunschalgorithm (Needleman and Wunsch, 1970, J. Mol. Biol. 48: 443-453) asimplemented in the Needle program of EMBOSS with gap open penalty of 10,gap extension penalty of 0.5, and the EBLOSUM62 matrix. The output ofNeedle labeled “longest identity” is used as the percent identity and iscalculated as follows:

(Identical Residues×100)/(Length of Alignment−Number of Gaps inAlignment)

For purposes of the present invention, the degree of identity betweentwo nucleotide sequences is determined using the Needleman-Wunschalgorithm (Needleman and Wunsch, 1970, J. Mol. Biol. 48: 443-453) asimplemented in the Needle program of EMBOSS with gap open penalty of 10,gap extension penalty of 0.5, and the EDNAFULL matrix. The output ofNeedle labeled “longest identity” is used as the percent identity and iscalculated as follows:

(Identical Residues×100)/(Length of Alignment−Number of Gaps inAlignment)

Homologous sequence: The term “homologous sequence” is defined herein asa predicted protein which gives an E value (or expectancy score) of lessthan 0.001 in a fasta search (Pearson, W. R., 1999, in BioinformaticsMethods and Protocols, S. Misener and S. A. Krawetz, ed., pp. 185-219)with SEQ ID NO: 2 or SEQ ID NO: 4.

Polypeptide fragment: The term “polypeptide fragment” is defined hereinas a polypeptide having one or more amino acids deleted from the aminoand/or carboxyl terminus of the mature polypeptide of SEQ ID NO: 2 orSEQ ID NO: 4; or a homologous sequence thereof; wherein the fragment hasendoglucanase activity. In a preferred aspect, a fragment contains atleast 320 amino acid residues, more preferably at least 340 amino acidresidues, and most preferably at least 360 amino acid residues of themature polypeptide of SEQ ID NO: 2 or a homologous sequence thereof. Inanother preferred aspect, a fragment contains at least 320 amino acidresidues, more preferably at least 340 amino acid residues, and mostpreferably at least 360 amino acid residues of the mature polypeptide ofSEQ ID NO: 4 or a homologous sequence thereof.

Subsequence: The term “subsequence” is defined herein as a nucleotidesequence having one or more nucleotides deleted from the 5′ and/or 3′end of the mature polypeptide coding sequence of SEQ ID NO: 1 or SEQ IDNO: 3; or a homologous sequence thereof; wherein the subsequence encodesa polypeptide fragment having endoglucanase activity. In a preferredaspect, a subsequence contains at least 960 nucleotides, more preferablyat least 1020 nucleotides, and most preferably at least 1080 nucleotidesof the mature polypeptide coding sequence of SEQ ID NO: 1 or ahomologous sequence thereof. In another preferred aspect, a subsequencecontains at least 960 nucleotides, more preferably at least 1020nucleotides, and most preferably at least 1080 nucleotides of the maturepolypeptide coding sequence of SEQ ID NO: 3 or a homologous sequencethereof.

Allelic variant: The term “allelic variant” denotes herein any of two ormore alternative forms of a gene occupying the same chromosomal locus.Allelic variation arises naturally through mutation, and may result inpolymorphism within populations. Gene mutations can be silent (no changein the encoded polypeptide) or may encode polypeptides having alteredamino acid sequences. An allelic variant of a polypeptide is apolypeptide encoded by an allelic variant of a gene.

Isolated polynucleotide: The term “isolated polynucleotide” as usedherein refers to a polynucleotide which is at least 20% pure, preferablyat least 40% pure, more preferably at least 60% pure, even morepreferably at least 80% pure, most preferably at least 90% pure, andeven most preferably at least 95% pure, as determined by agaroseelectrophoresis.

Substantially pure polynucleotide: The term “substantially purepolynucleotide” as used herein refers to a polynucleotide preparationfree of other extraneous or unwanted nucleotides and in a form suitablefor use within genetically engineered protein production systems. Thus,a substantially pure polynucleotide contains at most 10%, preferably atmost 8%, more preferably at most 6%, more preferably at most 5%, morepreferably at most 4%, more preferably at most 3%, even more preferablyat most 2%, most preferably at most 1%, and even most preferably at most0.5% by weight of other polynucleotide material with which it isnatively or recombinantly associated. A substantially purepolynucleotide may, however, include naturally occurring 5′ and 3′untranslated regions, such as promoters and terminators. It is preferredthat the substantially pure polynucleotide is at least 90% pure,preferably at least 92% pure, more preferably at least 94% pure, morepreferably at least 95% pure, more preferably at least 96% pure, morepreferably at least 97% pure, even more preferably at least 98% pure,most preferably at least 99%, and even most preferably at least 99.5%pure by weight. The polynucleotides of the present invention arepreferably in a substantially pure form. In particular, it is preferredthat the polynucleotides disclosed herein are in “essentially pureform”, i.e., that the polynucleotide preparation is essentially free ofother polynucleotide material with which it is natively or recombinantlyassociated. Herein, the term “substantially pure polynucleotide” issynonymous with the terms “isolated polynucleotide” and “polynucleotidein isolated form.” The polynucleotides may be of genomic, cDNA, RNA,semisynthetic, synthetic origin, or any combinations thereof.

Coding sequence: When used herein the term “coding sequence” means anucleotide sequence, which directly specifies the amino acid sequence ofits protein product. The boundaries of the coding sequence are generallydetermined by an open reading frame, which usually begins with the ATGstart codon or alternative start codons such as GTG and TTG and endswith a stop codon such as TAA, TAG, and TGA. The coding sequence may bea DNA, cDNA, or recombinant nucleotide sequence.

Mature polypeptide coding sequence: The term “mature polypeptide codingsequence” is defined herein as a nucleotide Sequence that encodes amature polypeptide having endoglucanase activity.

cDNA: The term “cDNA” is defined herein as a DNA molecule which can beprepared by reverse transcription from a mature, spliced, mRNA moleculeobtained from a eukaryotic cell. cDNA lacks intron sequences that areusually present in the corresponding genomic DNA. The initial, primaryRNA transcript is a precursor to mRNA which is processed through aseries of steps before appearing as mature spliced mRNA. These stepsinclude the removal of intron sequences by a process called splicing.cDNA derived from mRNA lacks, therefore, any intron sequences.

Nucleic acid construct: The term “nucleic acid construct” as used hereinrefers to a nucleic acid molecule, either single- or double-stranded,which is isolated from a naturally occurring gene or which is modifiedto contain segments of nucleic acids in a manner that would nototherwise exist in nature. The term nucleic acid construct is synonymouswith the term “expression cassette” when the nucleic acid constructcontains the control sequences required for expression of a codingsequence of the present invention.

Control sequence: The term “control sequences” is defined herein toinclude all components, which are necessary or advantageous for theexpression of a polynucleotide encoding a polypeptide of the presentinvention. Each control sequence may be native or foreign to thenucleotide sequence encoding the polypeptide or native or foreign toeach other. Such control sequences include, but are not limited to, aleader, polyadenylation sequence, propeptide sequence, promoter, signalpeptide sequence, and transcription terminator. At a minimum, thecontrol sequences include a promoter, and transcriptional andtranslational stop signals. The control sequences may be provided withlinkers for the purpose of introducing specific restriction sitesfacilitating ligation of the control sequences with the coding region ofthe nucleotide sequence encoding a polypeptide.

Operably linked: The term “operably linked” denotes herein aconfiguration in which a control sequence is placed at an appropriateposition relative to the coding sequence of the polynucleotide sequencesuch that the control sequence directs the expression of the codingsequence of a polypeptide.

Expression: The term “expression” includes any step involved in theproduction of the polypeptide including, but not limited to,transcription, post-transcriptional modification, translation,post-translational modification, and secretion.

Expression vector: The term “expression vector” is defined herein as alinear or circular DNA molecule that comprises a polynucleotide encodinga polypeptide of the present invention, and which is operably linked toadditional nucleotides that provide for its expression.

Host cell: The term “host cell”, as used herein, includes any cell typewhich is susceptible to transformation, transfection, transduction, andthe like with a nucleic acid construct or expression vector comprising apolynucleotide of the present invention.

Modification: The term “modification” means herein any chemicalmodification of the polypeptide consisting of the mature polypeptide ofSEQ ID NO: 2 or SEQ ID NO: 4; or a homologous sequence thereof; as wellas genetic manipulation of the DNA encoding such a polypeptide. Themodification can be substitutions, deletions and/or insertions of one ormore amino acids as well as replacements of one or more amino acid sidechains.

Artificial variant: When used herein, the term “artificial variant”means a polypeptide having endoglucanase activity produced by anorganism expressing a modified nucleotide sequence of the maturepolypeptide coding sequence of SEQ ID NO: 1 or SEQ ID NO: 3; or ahomologous sequence thereof. The modified nucleotide sequence isobtained through human intervention by modification of the nucleotidesequence disclosed in SEQ ID NO: 1 or SEQ ID NO: 3; or a homologoussequence thereof.

DETAILED DESCRIPTION OF THE INVENTION Polypeptides Having EndoglucanaseActivity

In a first aspect, the present invention relates to isolatedpolypeptides comprising an amino acid sequence having a degree ofidentity to the mature polypeptide of SEQ ID NO: 2 or SEQ ID NO: 4 of atleast 60%, preferably at least 65%, more preferably at least 70%, morepreferably at least 75%, more preferably at least 80%, more preferablyat least 85%, even more preferably at least 90%, most preferably atleast 95%, and even most preferably at least 96%, 97%, 98%, or 99%,which have endoglucanase activity (hereinafter “homologouspolypeptides”). In a preferred aspect, the homologous polypeptides havean amino acid sequence which differs by ten amino acids, preferably byfive amino acids, more preferably by four amino acids, even morepreferably by three amino acids, most preferably by two amino acids, andeven most preferably by one amino acid from the mature polypeptide ofSEQ ID NO: 2 or SEQ ID NO: 4.

A polypeptide of the present invention preferably comprises the aminoacid sequence of SEQ ID NO: 2 or an allelic variant thereof; or afragment thereof that has endoglucanase activity. In a preferred aspect,a polypeptide comprises the amino acid sequence of SEQ ID NO: 2. Inanother preferred aspect, a polypeptide comprises the mature polypeptideof SEQ ID NO: 2. In another preferred aspect, a polypeptide comprisesamino acids 19 to 396 of SEQ ID NO: 2, or an allelic variant thereof; ora fragment thereof that has endoglucanase activity. In another preferredaspect, a polypeptide comprises amino acids 19 to 396 of SEQ ID NO: 2.In another preferred aspect, a polypeptide consists of the amino acidsequence of SEQ ID NO: 2 or an allelic variant thereof; or a fragmentthereof that has endoglucanase activity. In another preferred aspect, apolypeptide consists of the amino acid sequence of SEQ ID NO: 2. Inanother preferred aspect, a polypeptide consists of the maturepolypeptide of SEQ ID NO: 2. In another preferred aspect, a polypeptideconsists of amino acids 19 to 396 of SEQ ID NO: 2 or an allelic variantthereof; or a fragment thereof that has endoglucanase activity. Inanother preferred aspect, a polypeptide consists of amino acids 19 to396 of SEQ ID NO: 2.

A polypeptide of the present invention preferably comprises the aminoacid sequence of SEQ ID NO: 4 or an allelic variant thereof; or afragment thereof that has endoglucanase activity. In a preferred aspect,a polypeptide comprises the amino acid sequence of SEQ ID NO: 4. Inanother preferred aspect, a polypeptide comprises the mature polypeptideof SEQ ID NO: 4. In another preferred aspect, a polypeptide comprisesamino acids 20 to 400 of SEQ ID NO: 4, or an allelic variant thereof; ora fragment thereof that has endoglucanase activity. In another preferredaspect, a polypeptide comprises amino acids 20 to 400 of SEQ ID NO: 4.In another preferred aspect, a polypeptide consists of the amino acidsequence of SEQ ID NO: 4 or an allelic variant thereof; or a fragmentthereof that has endoglucanase activity. In another preferred aspect, apolypeptide consists of the amino acid sequence of SEQ ID NO: 4. Inanother preferred aspect, a polypeptide consists of the maturepolypeptide of SEQ ID NO: 4. In another preferred aspect, a polypeptideconsists of amino acids 20 to 400 of SEQ ID NO: 4 or an allelic variantthereof; or a fragment thereof that has endoglucanase activity. Inanother preferred aspect, a polypeptide consists of amino acids 20 to400 of SEQ ID NO: 4.

In a second aspect, the present invention relates to isolatedpolypeptides having endoglucanase activity which are encoded bypolynucleotides which hybridize under very low stringency conditions,preferably low stringency conditions, more preferably medium stringencyconditions, more preferably medium-high stringency conditions, even morepreferably high stringency conditions, and most preferably very highstringency conditions with (i) the mature polypeptide coding sequence ofSEQ ID NO: 1 or SEQ ID NO: 3, (ii) the cDNA sequence contained in themature polypeptide coding sequence of SEQ ID NO: 1 or the genomic DNAsequence comprising the mature polypeptide coding sequence of SEQ ID NO:3, (iii) a subsequence of (i) or (ii), or (iv) a complementary strand of(i), (ii), or (iii) (J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989,Molecular Cloning, A Laboratory Manual, 2d edition, Cold Spring Harbor,N.Y.). A subsequence of the mature polypeptide coding sequence of SEQ IDNO: 1 or SEQ ID NO: 3 contains at least 100 contiguous nucleotides orpreferably at least 200 contiguous nucleotides. Moreover, thesubsequence may encode a polypeptide fragment which has endoglucanaseactivity. In a preferred aspect, the mature polypeptide coding sequenceis nucleotides 110 to 1557 of SEQ ID NO: 1. In another preferred aspect,the mature polypeptide coding sequence is nucleotides 58 to 1200 of SEQID NO: 3. In another preferred aspect, the complementary strand is thefull-length complementary strand of the mature polypeptide codingsequence of SEQ ID NO: 1 or SEQ ID NO: 3.

The nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 3; or asubsequence thereof; as well as the amino acid sequence of SEQ ID NO: 2or SEQ ID NO: 4; or a fragment thereof; may be used to design a nucleicacid probe to identify and clone DNA encoding polypeptides havingendoglucanase activity from strains of different genera or speciesaccording to methods well known in the art. In particular, such probescan be used for hybridization with the genomic or cDNA of the genus orspecies of interest, following standard Southern blotting procedures, inorder to identify and isolate the corresponding gene therein. Suchprobes can be considerably shorter than the entire sequence, but shouldbe at least 14, preferably at least 25, more preferably at least 35, andmost preferably at least 70 nucleotides in length. It is, however,preferred that the nucleic acid probe is at least 100 nucleotides inlength. For example, the nucleic acid probe may be at least 200nucleotides, preferably at least 300 nucleotides, more preferably atleast 400 nucleotides, or most preferably at least 500 nucleotides inlength. Even longer probes may be used, e.g., nucleic acid probes whichare at least 600 nucleotides, at least preferably at least 700nucleotides, more preferably at least 800 nucleotides, or mostpreferably at least 900 nucleotides in length. Both DNA and RNA probescan be used. The probes are typically labeled for detecting thecorresponding gene (for example, with ³²P, ³H, ³⁵S, biotin, or avidin).Such probes are encompassed by the present invention.

A genomic DNA or cDNA library prepared from such other strains may,therefore, be screened for DNA which hybridizes with the probesdescribed above and which encodes a polypeptide having endoglucanaseactivity. Genomic or other DNA from such other strains may be separatedby agarose or polyacrylamide gel electrophoresis, or other separationtechniques. DNA from the libraries or the separated DNA may betransferred to and immobilized on nitrocellulose or other suitablecarrier material. In order to identify a clone or DNA which ishomologous with SEQ ID NO; 1 or SEQ ID NO: 3; or a subsequence thereof;the carrier material is preferably used in a Southern blot.

For purposes of the present invention, hybridization indicates that thenucleotide sequence hybridizes to a labeled nucleic acid probecorresponding to the mature polypeptide coding sequence of SEQ ID NO: 1or SEQ ID NO: 3; the cDNA sequence contained in the mature polypeptidecoding sequence of SEQ ID NO: 1 or the genomic DNA sequence comprisingthe mature polypeptide coding sequence of SEQ ID NO: 3, itscomplementary strand; or a subsequence thereof; under very low to veryhigh stringency conditions. Molecules to which the nucleic acid probehybridizes under these conditions can be detected using, for example,X-ray film.

In a preferred aspect, the nucleic acid probe is the mature polypeptidecoding sequence of SEQ ID NO: 1. In another preferred aspect, thenucleic acid probe is nucleotides 110 to 1557 of SEQ ID NO: 1. Inanother preferred aspect, the nucleic acid probe is a polynucleotidesequence which encodes the polypeptide of SEQ ID NO: 2, or a subsequencethereof. In another preferred aspect, the nucleic acid probe is SEQ IDNO: 1. In another preferred aspect, the nucleic acid probe is thepolynucleotide sequence contained in plasmid pPH47 which is contained inE. coli NRRL B-30898, wherein the polynucleotide sequence thereofencodes a polypeptide having endoglucanase activity. In anotherpreferred aspect, the nucleic acid probe is the mature polypeptidecoding region contained in plasmid pPH47 which is contained in E. coliNRRL B-30898.

In a preferred aspect, the nucleic acid probe is the mature polypeptidecoding sequence of SEQ ID NO: 3. In another preferred aspect, thenucleic acid probe is nucleotides 58 to 1200 of SEQ ID NO: 3. In anotherpreferred aspect, the nucleic acid probe is a polynucleotide sequencewhich encodes the polypeptide of SEQ ID NO: 4, or a subsequence thereof.In another preferred aspect, the nucleic acid probe is SEQ ID NO: 3. Inanother preferred aspect, the nucleic acid probe is the polynucleotidesequence contained in plasmid pCIBG146 which is contained in E. coliNRRL B-30901, wherein the polynucleotide sequence thereof encodes apolypeptide having endoglucanase activity. In another preferred aspect,the nucleic acid probe is the mature polypeptide coding region containedin plasmid pCIBG146 which is contained in E. coli NRRL B-30901.

For long probes of at least 100 nucleotides in length, very low to veryhigh stringency conditions are defined as prehybridization andhybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 μg/ml sheared anddenatured salmon sperm DNA, and either 25% formamide for very low andlow stringencies, 35% formamide for medium and medium-high stringencies,or 50% formamide for high and very high stringencies, following standardSouthern blotting procedures for 12 to 24 hours optimally.

For long probes of at least 100 nucleotides in length, the carriermaterial is filially washed three times each for 15 minutes using 2×SSC,0.2% SDS preferably at least at 45° C. (very low stringency), morepreferably at least at 50° C. (low stringency), more preferably at leastat 55° C. (medium stringency), more preferably at least at 60° C.(medium-high stringency), even more preferably at least at 65° C. (highstringency), and most preferably at least at 70° C. (very highstringency).

For short probes which are about 15 nucleotides to about 70 nucleotidesin length, stringency conditions are defined as prehybridization,hybridization, and washing post-hybridization at about 5° C. to about10° C. below the calculated T_(m) using the calculation according toBolton and McCarthy (1962, Proceedings of the National Academy ofSciences USA 48:1390) in 0.9 M NaCl, 0.09 M Tris-HCl pH 7.6, 6 mM EDTA,0.5% NP-40, 1×Denhardt's solution, 1 mM sodium pyrophosphate, 1 mMsodium monobasic phosphate, 0.1 mM ATP, and 0.2 mg of yeast RNA per mlfollowing standard Southern blotting procedures for 12 to 24 hoursoptimally.

For short probes which are about 15 nucleotides to about 70 nucleotidesin length, the carrier material is washed once in 6×SCC plus 0.1% SDSfor 15 minutes and twice each for 15 minutes using 6×SSC at 5° C. to 10°C. below the calculated T_(m).

In a third aspect, the present invention relates to isolatedpolypeptides encoded by polynucleotides comprising or consisting ofnucleotide sequences which have a degree of identity to the maturepolypeptide coding sequence of SEQ ID NO: 1 or SEQ ID NO: 3 of at least60%, preferably at least 65%, more preferably at least 70%, morepreferably at least 75%, more preferably at least 80%, more preferablyat least 85%, more preferably at least 90%, even more preferably atleast 95%, and most preferably at least 97% identity, which encode anactive polypeptide. In a preferred aspect, the mature polypeptide codingsequence is nucleotides 110 to 1557 of SEQ ID NO: 1. In anotherpreferred aspect, the mature polypeptide coding sequence is nucleotides58 to 1200 of SEQ ID NO: 3. See polynucleotide section herein.

In a fourth aspect, the present invention relates to artificial variantscomprising a substitution, deletion, and/or insertion of one or more (orseveral) amino acids of the mature polypeptide of SEQ ID NO: 2 or SEQ IDNO: 4; or a homologous sequence thereof. Preferably, amino acid changesare of a minor nature, that is conservative amino acid substitutions orinsertions that do not significantly affect the folding and/or activityof the protein; small deletions, typically of one to about 30 aminoacids; small amino- or carboxyl-terminal extensions, such as anamino-terminal methionine residue; a small linker peptide of up to about20-25 residues; or a small extension that facilitates purification bychanging net charge or another function, such as a poly-histidine tract,an antigenic epitope or a binding domain.

Examples of conservative substitutions are within the group of basicamino acids (arginine, lysine and histidine), acidic amino acids(glutamic acid and aspartic acid), polar amino acids (glutamine andasparagine), hydrophobic amino acids (leucine, isoleucine and valine),aromatic amino acids (phenylalanine, tryptophan and tyrosine), and smallamino acids (glycine, alanine, serine, threonine and methionine). Aminoacid substitutions which do not generally alter specific activity areknown in the art and are described, for example, by H. Neurath and R. L.Hill, 1979, In, The Proteins, Academic Press, New York. The mostcommonly occurring exchanges are Ala/Ser, Val/Ile, Asp/Glu, Thr/Ser,Ala/Gly, Ala/Thr, Ser/Asn, Ala/Val, Ser/Gly, Tyr/Phe, Ala/Pro, Lys/Arg,Asp/Asn, Leu/Ile, Leu/Val, Ala/Glu, and Asp/Gly.

In addition to the 20 standard amino acids, non-standard amino acids(such as 4-hydroxyproline, 6-N-methyl lysine, 2-aminoisobutyric acid,isovaline, and alpha-methyl serine) may be substituted for amino acidresidues of a wild-type polypeptide. A limited number ofnon-conservative amino acids, amino acids that are not encoded by thegenetic code, and unnatural amino acids may be substituted for aminoacid residues, “Unnatural amino acids” have been modified after proteinsynthesis, and/or have a chemical structure in their side chain(s)different from that of the standard amino acids. Unnatural amino acidscan be chemically synthesized, and preferably, are commerciallyavailable, and include pipecolic acid, thiazolidine carboxylic acid,dehydroproline, 3- and 4-methylproline, and 3,3-dimethylproline.

Alternatively, the amino acid changes are of such a nature that thephysico-chemical properties of the polypeptides are altered. Forexample, amino acid changes may improve the thermal stability of thepolypeptide, alter the substrate specificity, change the pH optimum, andthe like.

Essential amino acids in the parent polypeptide can be identifiedaccording to procedures known in the art, such as site-directedmutagenesis or alanine-scanning mutagenesis (Cunningham and Wells, 1989,Science 244: 1081-1085). In the latter technique, single alaninemutations are introduced at every residue in the molecule, and theresultant mutant molecules are tested for biological activity (i.e.,endoglucanase activity) to identify amino acid residues that arecritical to the activity of the molecule. See also, Hilton et al., 1995,J. Biol. Chem. 271: 4699-4708. The active site of the enzyme or otherbiological interaction can also be determined by physical analysis ofstructure, as determined by such techniques as nuclear magneticresonance, crystallography, electron diffraction, or photoaffinitylabeling, in conjunction with mutation of putative contact site aminoacids. See, for example, de Vos et al., 1992, Science 255: 306-312;Smith et al., 1992, J. Mol. Biol. 224; 899-904; Wlodaver et al., 1992,FEBS Lett. 309: 59-64. The identities of essential amino acids can alsobe inferred from analysis of identities with polypeptides which arerelated to a polypeptide according to the invention.

Single or multiple amino acid substitutions, deletions, and/orinsertions can be made and tested using known methods of mutagenesis,recombination, and/or shuffling, followed by a relevant screeningprocedure, such as those disclosed by Reidhaar-Olson and Sauer, 1988,Science 241: 53-57; Bowie and Sauer, 1989, Proc. Natl. Acad. Sal. USA86: 2152-2156; WO 95/17413; or WO 95/22625. Other methods that can beused include error-prone PCR, phage display (e.g., Lowman et al., 1991,Biochem. 30: 10832-10837; U.S. Pat. No. 5,223,409; WO 92/06204), andregion-directed mutagenesis (Derbyshire et al., 1986, Gene 46: 145; Neret al., 1988, DNA 7: 127).

Mutagenesis/shuffling methods can be combined with high-throughput,automated screening methods to detect activity of cloned, mutagenizedpolypeptides expressed by host cells (Ness et al., 1999, NatureBiotechnology 17: 893-896). Mutagenized DNA molecules that encode activepolypeptides can be recovered from the host cells and rapidly sequencedusing standard methods in the art. These methods allow the rapiddetermination of the importance of individual amino acid residues in apolypeptide of interest, and can be applied to polypeptides of unknownstructure.

The total number of amino acid substitutions, deletions and/orinsertions of the mature polypeptide of SEQ ID NO: 2 or SEQ ID NO: 4,such as amino acids 19 to 396 of SEQ ID NO: 2 or amino acids 20 to 400of SEQ ID NO: 4, is 10, preferably 9, more preferably 8, more preferably7, more preferably at most 6, more preferably 5, more preferably 4, evenmore preferably 3, most preferably 2, and even most preferably 1.

Sources of Polypeptides Having Endoglucanase Activity

A polypeptide of the present invention may be obtained frommicroorganisms of any genus. For purposes of the present invention, theterm “obtained from” as used herein in connection with a given sourceshall mean that the polypeptide encoded by a nucleotide sequence isproduced by the source or by a strain in which the nucleotide sequencefrom the source has been inserted. In a preferred aspect, thepolypeptide obtained from a given source is secreted extracellularly.

A polypeptide having endoglucanase activity of the present invention maybe a bacterial polypeptide. For example, the polypeptide may be a grampositive bacterial polypeptide such as a Bacillus, Streptococcus,Streptomyces, Staphylococcus, Enterococcus, Lactobacillus, Lactococcus,Clostridium, Geobacillus, or Oceanobacillus polypeptide havingendoglucanase activity, or a Gram negative bacterial polypeptide such asan E. coli, Pseudomonas, Salmonella, Campylobacter, Helicobacter,Flavobacterium, Fusobacterium, Ilyobacter, Neisseria, or Ureaplasmapolypeptide having endoglucanase activity.

In a preferred aspect, the polypeptide is a Bacillus alkalophilus,Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans,Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus,Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacilluspumilus, Bacillus stearothermophilus, Bacillus subtilis, or Bacillusthuringiensis polypeptide having endoglucanase activity.

In another preferred aspect, the polypeptide is a Streptococcusequisimilis, Streptococcus pyoaenes, Streptococcus uberis, orStreptococcus equi subsp. Zooepidemicus polypeptide having endoglucanaseactivity.

In another preferred aspect, the polypeptide is a Streptomycesachrotnogenes, Streptomyces avermitilis, Streptomyces coelicolor,Streptomyces griseus, or Streptomyces lividans polypeptide havingendoglucanase activity.

A polypeptide having endoglucanase activity of the present invention mayalso be a fungal polypeptide, and more preferably a yeast polypeptidesuch as a Candida, Kluyveromyces, Pichia, Saccharomyces,Schizosaccharomyces, or Yarrowia polypeptide having endoglucanaseactivity; or more preferably a filamentous fungal polypeptide such as anAcremonium, Aspergillus, Aureobasidium, Chtysosporium, Cryptococcus,Filibasidium, Fusarium, Humicola, Magnaporthe, Mucor, Myceliophthora,Neocallimastix, Neurospora, Paecilomyces, Penicillium, Piromyces,Schizophylium, Talaromyces, Thertnoascus, Thielavia, Tolypocladium, orTrichoderma polypeptide having endoglucanase activity.

In a preferred aspect, the polypeptide is a Saccharomycescarisbergensis, Saccharomyces cerevisiae, Saccharomyces diastaticus,Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomycesnorbensis, or Saccharomyces oviformis polypeptide having endoglucanaseactivity.

In another preferred aspect, the polypeptide is an Aspergillusaculeates, Aspergillus awamori, Aspergillus fumigatus, Aspergillusfoetidus, Aspergillus japonicus, Aspergillus nidulans, Aspergillusnicer, Aspergillus oryzae, Chrysosporium keratinophilum, Chrysosporiumlucknowense, Chrysosporium tropicum, Chrysosporium merdarium,Chrysosporium inops, Chrysosporium pannicola, Chrysosporiumqueenslandicum, Chrysosporium zonatum, Fusarium bactridioides, Fusariumcerealis, Fusarium crookwellense, Fusarium culmorum, Fusariumgraminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi,Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusariumsambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusariumsulphureum, Fusarium torulosum, Fusarium trichothecioides, Fusariumvenenatum, Humicola insolens, Humicola lanuginosa, Mucor miehei,Myceliophthora thermophila, Neurospora crassa, Penicillium brasilianum,Penicillium camembertii, Penicillium capsulatum, Penicilliumchrysogenum, Penicillium citreonigrum, Penicillium citrinum, Penicilliumclaviforme, Penicillium corylophilum, Penicillium crustosum, Penicilliumdigitatum, Penicillium expansum, Penicillium funiculosum, Penicilliumglabrum, Penicillium granulatum, Penicillium griseofulvum, Penicilliumislandicum, Penicillium italicum, Penicillium janthinellum, Penicilliumlividum, Penicillium megasporum, melinii, Penicillium notatum,Penicillium oxalicum, Penicillium puberulum, Penicillium purpurescens,Penicillium purpurogenum, Penicillium roquefortii, Penicilliumrugulosum, Penicillium spinulosum, Penicillium waksmanii, Trichodermaharzianum, Trichoderma koningii, Trichoderma longibrachiatum,Trichoderma reesei, or Trichoderma viride polypeptide havingendoglucanase activity.

In another preferred aspect, the polypeptide is a Thielavia achromatica,Thielavia albomyces, Thielavia albopilosa, Thielavia australeinsis,Thielavia fimeti, Thielavia microspora, Thielavia ovispora, Thielaviaperuviana, Thielavia spededonium, Thielavia setosa, Thielaviasubthermophda, Thielavia terrestris, Thielavia terricola, Thielaviathermophila, Thielavia variospora, or Thielavia wareingii polypeptidehaving endoglucanase activity.

In a more preferred aspect, the polypeptide is a Thielavia terrestrispolypeptide, and most preferably a Thielavia terrestris NRRL 8126polypeptide, e.g., the polypeptide of SEQ ID NO: 2 or SEQ ID NO: 4, orthe mature polypeptide thereof.

It will be understood that for the aforementioned species the inventionencompasses both the perfect and imperfect states, and other taxonomicequivalents, e.g., anamorphs, regardless of the species name by whichthey are known. Those skilled in the art will readily recognize theidentity of appropriate equivalents.

Strains of these species are readily accessible to the public in anumber of culture collections, such as the American Type CultureCollection (ATCC), Deutsche Sammlung von Mikroorganismen andZellkulturen GmbH (DSM), Centraalbureau Voor Schimmelcultures (CBS), andAgricultural Research Service Patent Culture Collection, NorthernRegional Research Center (NRRL).

Furthermore, such polypeptides may be identified and obtained from othersources including microorganisms isolated from nature (e.g., soil,composts, water, etc.) using the above-mentioned probes. Techniques forisolating microorganisms from natural habitats are well known in theart. The polynucleotide may then be obtained by similarly screening agenomic or cDNA library of such a microorganism. Once a polynucleotidesequence encoding a polypeptide has been detected with the probe(s), thepolynucleotide can be isolated or cloned by utilizing techniques whichare well known to those of ordinary skill in the art (see, e.g.,Sambrook et al., 1989, supra).

Polypeptides of the present invention also include fused polypeptides orcleavable fusion polypeptides in which another polypeptide is fused atthe N-terminus or the C-terminus of the polypeptide or fragment thereof.A fused polypeptide is produced by fusing a nucleotide sequence (or aportion thereof) encoding another polypeptide to a nucleotide sequence(or a portion thereof) of the present invention. Techniques forproducing fusion polypeptides are known in the art, and include ligatingthe coding sequences encoding the polypeptides so that they are in frameand that expression of the fused polypeptide is under control of thesame promoter(s) and terminator.

A fusion polypeptide can further comprise a cleavage site. Uponsecretion of the fusion protein, the site is cleaved releasing thepolypeptide having endoglucanase activity from the fusion protein.

Examples of cleavage sites include, but are not limited to, a Kex2 sitewhich encodes the dipeptide Lys-Arg (Martin at al., 2003, J. Ind.Microbiol. Biotechnol. 3: 568-76: Svetina at al., 2000, J. Biatechnol.76: 245-251; Rasmussen-Wilson et al., 1997, Appl. Environ. Microbial.63: 3488-3493; Ward et al., 1995, Biotechnology 13: 498-503; andContreras at al., 1991, Biotechnology 9: 378-381), an Ile-(Glu orAsp)-Gly-Arg site, which is cleaved by a Factor Xa protease after thearginine residue (Eaton et al., 1986, Biochem. 25: 505-512); aAsp-Asp-Asp-Asp-Lys site, which is cleaved by an enterokinase after thelysine (Collins-Racie et al., 1995, Biotechnology 13: 982-987); aHis-Tyr-Glu site or His-Tyr-Asp site, which is cleaved by Genenase I(Carter at al., 1989, Proteins: Structure, Function, and Genetics 6:240-248); a Leu-Val-Pro-Arg-Gly-Ser site, which is cleaved by thrombinafter the Arg (Stevens, 2003, Drug Discovery World 4: 35-48); aGlu-Asn-Leu-Tyr-Phe-Gln-Gly site, which is cleaved by TEV protease afterthe Gln (Stevens, 2003, supra); and a Leu-Glu-Val-Leu-Phe-Gln-Gly-Prosite, which is cleaved by a genetically engineered form of humanrhinovirus 30 protease after the Gln (Stevens, 2003, supra).

Polynucleotides

The present invention also relates to an isolated polynucleotidecomprising or consisting of a nucleotide sequence which encodes apolypeptide of the present invention having endoglucanase activity.

In a preferred aspect, the nucleotide sequence comprises or consists ofSEQ ID NO: 1. In another more preferred aspect, the nucleotide sequencecomprises or consists of the sequence contained in plasmid pPH47 whichis contained in E. coli NRRL B-30898. In another preferred aspect, thenucleotide sequence comprises or consists of the mature polypeptidecoding region of SEQ ID NO: 1. In another preferred aspect, thenucleotide sequence comprises or consists of nucleotides 110 to 1557 ofSEQ ID NO: 1. In another more preferred aspect, the nucleotide sequencecomprises or consists of the mature polypeptide coding region containedin plasmid pPH47 which is contained in E. coli NRRL B-30898. The presentinvention also encompasses nucleotide sequences which encodepolypeptides comprising or consisting of the amino acid sequence of SEQID NO: 2 or the mature polypeptide thereof, which differ from SEQ ID NO:1 or the mature polypeptide coding sequence thereof by virtue of thedegeneracy of the genetic code. The present invention also relates tosubsequences of SEQ ID NO: 1 which encode fragments of SEQ ID NO: 2 thathave endoglucanase activity.

In another preferred aspect, the nucleotide sequence comprises orconsists of SEQ ID NO: 3. In another more preferred aspect, thenucleotide sequence comprises or consists of the sequence contained inplasmid pCIBG146 which is contained in E. coli NRRL B-30901. In anotherpreferred aspect, the nucleotide sequence comprises or consists of themature polypeptide coding region of SEQ ID NO: 3. In another preferredaspect, the nucleotide sequence comprises or consists of nucleotides 58to 1200 of SEQ ID NO: 3. In another more preferred aspect, thenucleotide sequence comprises or consists of the mature polypeptidecoding region contained in plasmid pCIBG146 which is contained in E.coli NRRL B-30901. The present invention also encompasses nucleotidesequences which encode polypeptides comprising or consisting of theamino acid sequence of SEQ ID NO: 4 or the mature polypeptide thereof,which differ from SEQ ID NO: 3 or the mature polypeptide coding sequencethereof by virtue of the degeneracy of the genetic code. The presentinvention also relates to subsequences of SEQ ID NO: 3 which encodefragments of SEQ ID NO: 4 that have endoglucanase activity.

The present invention also relates to mutant polynucleotides comprisingor consisting of at least one mutation in the mature polypeptide codingsequence of SEQ ID NO: 1 or SEQ ID NO: 3, in which the mutant nucleotidesequence encodes the mature polypeptide of SEQ ID NO: 2 or SEQ ID NO: 4.In a preferred aspect, the mature polypeptide is amino acids 19 to 396of SEQ ID NO: 2. In another preferred aspect, the mature polypeptide isamino acids 20 to 400 of SEQ ID NO: 4.

The techniques used to isolate or clone a polynucleotide encoding apolypeptide are known in the art and include isolation from genomic DNA,preparation from cDNA, or a combination thereof. The cloning of thepolynucleotides of the present invention from such genomic DNA can beeffected, e.g., by using the well known polymerase chain reaction (PCR)or antibody screening of expression libraries to detect cloned DNAfragments with shared structural features. See, e.g., Innis et al.,1990, PCR: A Guide to Methods and Application, Academic Press, New York.Other nucleic acid amplification procedures such as ligase chainreaction (LCR), ligated activated transcription (LAT) and nucleotidesequence-based amplification (NASBA) may be used. The polynucleotidesmay be cloned from a strain of Myceliophthora thermophila CBS 117.65,basidiomycete CBS 494.95, or basidiomycete CBS 495.95, or another orrelated organism and thus, for example, may be an allelic or speciesvariant of the polypeptide encoding region of the nucleotide sequence.

The present invention also relates to isolated polynucleotidescomprising or consisting of nucleotide sequences which have a degree ofidentity to the mature polypeptide coding sequence of SEQ ID NO: 1 orSEQ ID NO: 3 of at least 60%, preferably at least 65%, more preferablyat least 70%, more preferably at least 75%, more preferably at least80%, more preferably at least 85%, more preferably at least 90%, evenmore preferably at least 95%, and most preferably at least 97% identity,which encode an active polypeptide. In a preferred aspect, the maturepolypeptide coding sequence is nucleotides 110 to 1557 of SEQ ID NO: 1.In another preferred aspect, the mature polypeptide coding sequence isnucleotides 58 to 1200 of SEQ ID NO: 3.

Modification of a nucleotide sequence encoding a polypeptide of thepresent invention may be necessary for the synthesis of polypeptidessubstantially similar to the polypeptide. The term “substantiallysimilar” to the polypeptide refers to non-naturally occurring forms ofthe polypeptide. These polypeptides may differ in some engineered wayfrom the polypeptide isolated from its native source, e.g., artificialvariants that differ in specific activity, thermostability, pH optimum,or the like. The variant sequence may be constructed on the basis of thenucleotide sequence presented as the polypeptide encoding region of SEQID NO: 1 or SEQ ID NO: 3, e.g., a subsequence thereof, and/or byintroduction of nucleotide substitutions which do not give rise toanother amino acid sequence of the polypeptide encoded by the nucleotidesequence, but which correspond to the codon usage of the host organismintended for production of the enzyme, or by introduction of nucleotidesubstitutions which may give rise to a different amino acid sequence.For a general description of nucleotide substitution, see, e.g., Ford etal., 1991, Protein Expression and Purification 2: 95-107.

It will be apparent to those skilled in the art that such substitutionscan be made outside the regions critical to the function of the moleculeand still result in an active polypeptide. Amino acid residues essentialto the activity of the polypeptide encoded by an isolated polynucleotideof the invention, and therefore preferably not subject to substitution,may be identified according to procedures known in the art, such assite-directed mutagenesis or alanine-scanning mutagenesis (see, e.g.,Cunningham and Wells, 1989, supra). In the latter technique, mutationsare introduced at every positively charged residue in the molecule, andthe resultant mutant molecules are tested for endoglucanase activity toidentify amino acid residues that are critical to the activity of themolecule. Sites of substrate-enzyme interaction can also be determinedby analysis of the three-dimensional structure as determined by suchtechniques as nuclear magnetic resonance analysis, crystallography orphotoaffinity labeling (see, e.g., de Vos et al., 1992, supra; Smith etal., 1992, supra; Wlodaver et al., 1992, supra).

The present invention also relates to isolated polynucleotides encodinga polypeptide of the present invention, which hybridize under very lowstringency conditions, preferably low stringency conditions, morepreferably medium stringency conditions, more preferably medium-highstringency conditions, even more preferably high stringency conditions,and most preferably very high stringency conditions with under at leasthigh stringency conditions with (i) the mature polypeptide codingsequence of SEQ ID NO: 1 or SEQ ID NO: 3, (ii) the cDNA sequencecontained in the mature polypeptide coding sequence of SEQ ID NO: 1 orthe genomic DNA sequence comprising the mature polypeptide codingsequence of SEQ ID NO: 3, (iii) a subsequence of (i) or (ii), or (iv) acomplementary strand of (i), (ii), or (iii); or allelic variants thereof(Sambrook et al., 1989, supra), as defined herein. In a preferredaspect, the mature polypeptide coding sequence is nucleotides 110 to1557 of SEQ ID NO: 1. In another preferred aspect, the maturepolypeptide coding sequence is nucleotides 58 to 1200 of SEQ ID NO: 3.In another preferred aspect, the complementary strand is the full-lengthcomplementary strand of the mature polypeptide coding sequence of SEQ IDNO: 1 or SEQ ID NO: 3.

The present invention also relates to isolated polynucleotides obtainedby (a) hybridizing a population of DNA under very low, low, medium,medium-high, high, or very high stringency conditions with (i) themature polypeptide coding sequence of SEQ ID NO: 1 or SEQ ID NO: 3, (ii)the cDNA sequence contained in the mature polypeptide coding sequence ofSEQ ID NO: 1 or the genomic DNA sequence comprising the maturepolypeptide coding sequence of SEQ ID NO: 3, or (iii) a complementarystrand of (i) or (ii); and (b) isolating the hybridizing polynucleotide,which encodes a polypeptide having endoglucanase activity. In apreferred aspect, the mature polypeptide coding sequence is nucleotides110 to 1557 of SEQ ID NO: 1. In another preferred aspect, the maturepolypeptide coding sequence is nucleotides 58 to 1200 of SEQ ID NO: 3.In another preferred aspect, the complementary strand is the full-lengthcomplementary strand of the mature polypeptide coding sequence of SEQ IDNO: 1 or SEQ ID NO: 3.

Nucleic Acid Constructs

The present invention also relates to nucleic acid constructs comprisingan isolated polynucleotide of the present invention operably linked toone or more control sequences that direct the expression of the codingsequence in a suitable host cell under conditions compatible with thecontrol sequences.

An isolated polynucleotide encoding a polypeptide of the presentinvention may be manipulated in a variety of ways to provide forexpression of the polypeptide. Manipulation of the polynucleotide'ssequence prior to its insertion into a vector may be desirable ornecessary depending on the expression vector. The techniques formodifying polynucleotide sequences utilizing recombinant DNA methods arewell known in the art.

The control sequence may be an appropriate promoter sequence, anucleotide sequence which is recognized by a host cell for expression ofa polynucleotide encoding a polypeptide of the present invention. Thepromoter sequence contains transcriptional control sequences whichmediate the expression of the polypeptide. The promoter may be anynucleotide sequence which shows transcriptional activity in the hostcell of choice including mutant, truncated, and hybrid promoters, andmay be obtained from genes encoding extracellular or intracellularpolypeptides either homologous or heterologous to the host cell.

Examples of suitable promoters for directing the transcription of thenucleic acid constructs of the present invention, especially in abacterial host cell, are the promoters obtained from the E. coli lacoperon, Streptomyces coelicolor agarase gene (dagA), Bacillus subtilislevansucrase gene (sacB), Bacillus licheniformis alpha-amylase gene(amyl), Bacillus stearothermophilus maltogenic amylase gene (amyl),Bacillus amyloliquefaciens alpha-amylase gene (amyQ), Bacilluslicheniformis penicillinase gene (penP), Bacillus subtilis xylA and xylBgenes, and prokaryotic beta-lactamase gene (Villa-Kamaroff at al., 1978,Proceedings of the National Academy of Sciences USA 75: 3727-3731), aswell as the tac promoter (DeBoer at al., 1983, Proceedings of theNational Academy of Sciences USA 80: 21-25). Further promoters aredescribed in “Useful proteins from recombinant bacteria” in ScientificAmerican, 1980, 242: 74-94; and in Sambrook et al., 1989, supra.

Examples of suitable promoters for directing the transcription of thenucleic acid constructs of the present invention in a filamentous fungalhost cell are promoters obtained from the genes for Aspergillus oryzaeTAKA amylase, Rhizomucor miehei aspartic proteinase, Aspergillus nigerneutral alpha-amylase, Aspergillus niger acid stable alpha-amylase,Aspergillus niger or Aspergillus awamori glucoamylase (glaA), Rhizomucormiehei lipase, Aspergillus oryzae alkaline protease, Aspergillus oryzaetriose phosphate isomerase, Aspergillus nidulans acetamidase, Fusariumvenenatum amyloglucosidase (WO 00/56900), Fusarium venenatum Daria (WO00/56900), Fusarium venenatum Quinn (WO 00/56900), Fusarium oxysporumtrypsin-like protease (WO 96/00787), Trichoderma reeseibeta-glucosidase, Trichoderma reesei cellobiohydrolase I, Trichodermareesei cellobiohydrolase II, Trichoderma reesei endoglucanase I,Trichoderma reesei endoglucanase II, Trichoderma reesei endoglucanaseIII, Trichoderma reesei endoglucanase IV, Trichoderma reeseiendoglucanase V, Trichoderma reesei xylanase I, Trichoderma reeseixylanase II, Trichoderma reesei beta-xylosidase, as well as the NA2-tpipromoter (a hybrid of the promoters from the genes for Aspergillus nigerneutral alpha-amylase and Aspergillus oryzae triose phosphateisomerase); and mutant, truncated, and hybrid promoters thereof.

In a yeast host, useful promoters are obtained from the genes forSaccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiaegalactokinase (GAL1), Saccharomyces cerevisiae alcoholdehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH1, ADH2/GAP),Saccharomyces cerevisiae triose phosphate isomerase (TP1), Saccharomycescerevisiae metallothionein (CUP1), and Saccharomyces cerevisiae3-phosphoglycerate kinase.

Other useful promoters for yeast host cells are described by Romanos etal., 1992, Yeast 8: 423-488.

The control sequence may also be a suitable transcription terminatorsequence, a sequence recognized by a host cell to terminatetranscription. The terminator sequence is operably linked to the 3′terminus of the nucleotide sequence encoding the polypeptide. Anyterminator which is functional in the host cell of choice may be used inthe present invention.

Preferred terminators for filamentous fungal host cells are obtainedfrom the genes for Aspergillus oryzae TAKA amylase, Aspergillus nigerglucoamylase, Aspergillus nidulans anthranilate synthase, Aspergillusniger alpha-glucosidase, and Fusarium oxysporum trypsin-like protease.

Preferred terminators for yeast host cells are obtained from the genesfor Saccharomyces cerevisiae enolase, Saccharomyces cerevisiaecytochrome C (CYC1), and Saccharomyces cerevisiaeglyceraldehyde-3-phosphate dehydrogenase. Other useful terminators foryeast host cells are described by Romanos et al., 1992, supra.

The control sequence may also be a suitable leader sequence, anontranslated region of an mRNA which is important for translation bythe host cell. The leader sequence is operably linked to the 5′ terminusof the nucleotide sequence encoding the polypeptide. Any leader sequencethat is functional in the host cell of choice may be used in the presentinvention.

Preferred leaders for filamentous fungal host cells are obtained fromthe genes for Aspergillus oryzae TAKA amylase and Aspergillus nidulanstriose phosphate isomerase.

Suitable leaders for yeast host cells are obtained from the genes forSaccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae3-phosphoglycerate kinase, Saccharomyces cerevisiae alpha-factor, andSaccharomyces cerevisiae alcoholdehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP).

The control sequence may also be a polyadenylation sequence, a sequenceoperably linked to the 3′ terminus of the nucleotide sequence and which,when transcribed, is recognized by the host cell as a signal to addpolyadenosine residues to transcribed mRNA. Any polyadenylation sequencewhich is functional in the host cell of choice may be used in thepresent invention.

Preferred polyadenylation sequences for filamentous fungal host cellsare obtained from the genes for Aspergillus oryzae TAKA amylase,Aspergillus niger glucoamylase, Aspergillus nidulans anthranilatesynthase, Fusarium oxysporum trypsin-like protease, and Aspergillusniger alpha-glucosidase.

Useful polyadenylation sequences for yeast host cells are described byGuo and Sherman, 1995, Molecular Cellular Biology 15: 5983-5990.

The control sequence may also be a signal peptide coding region thatcodes for an amino acid sequence linked to the amino terminus of apolypeptide and directs the encoded polypeptide into the cell'ssecretory pathway. The 5′ end of the coding sequence of the nucleotidesequence may inherently contain a signal peptide coding region naturallylinked in translation reading frame with the segment of the codingregion which encodes the secreted polypeptide. Alternatively, the 5′ endof the coding sequence may contain a signal peptide coding region whichis foreign to the coding sequence. The foreign signal peptide codingregion may be required where the coding sequence does not naturallycontain a signal peptide coding region. Alternatively, the foreignsignal peptide coding region may simply replace the natural signalpeptide coding region in order to enhance secretion of the polypeptide.However, any signal peptide coding region which directs the expressedpolypeptide into the secretory pathway of a host cell of choice, i.e.,secreted into a culture medium, may be used in the present invention.

Effective signal peptide coding regions for bacterial host cells are thesignal peptide coding regions obtained from the genes for Bacillus NCIB11837 maltogenic amylase, Bacillus stearothermophilus alpha-amylase,Bacillus licheniformis subtilisin. Bacillus licheniformisbeta-lactamase, Bacillus stearothermophilus neutral proteases (nprT,nprS, nprM), and Bacillus subtilis prsA. Further signal peptides aredescribed by Simonen and Palva, 1993, Microbiological Reviews 57:109-137.

Effective signal peptide coding regions for filamentous fungal hostcells are the signal peptide coding regions obtained from the genes forAspergillus oryzae TAKA amylase, Aspergillus niger neutral amylase,Aspergillus niger glucoamylase, Rhizomucor miehei aspartic proteinase,Humicola insolens cellulase, Humicola insolens endoglucanase V, andHumicola lanuginosa lipase.

Useful signal peptides for yeast host cells are obtained from the genesfor Saccharomyces cerevisiae alpha-factor and Saccharomyces cerevisiaeinvertase. Other useful signal peptide coding regions are described byRomanos et al., 1992, supra.

In a preferred aspect, the signal peptide comprises or consists of aminoacids 1 to 18 of SEQ ID NO: 2. In another preferred aspect, the signalpeptide coding region is nucleotides 56 to 109 of SEQ ID NO: 1.

In another preferred aspect, the signal peptide comprises or consists ofamino acids 1 to 19 of SEQ ID NO: 4. In another preferred aspect, thesignal peptide coding region comprises or consists of nucleotides 1 to57 of SEQ ID NO: 3.

The control sequence may also be a propeptide coding region that codesfor an amino acid sequence positioned at the amino terminus of apolypeptide. The resultant polypeptide is known as a proenzyme orpropolypeptide (or a zymogen in some cases). A propeptide is generallyinactive and can be converted to a mature active polypeptide bycatalytic or autocatalytic cleavage of the propeptide from thepropolypeptide. The propeptide coding region may be obtained from thegenes for Bacillus subtilis alkaline protease (aprE), Bacillus subtilisneutral protease (nprT), Saccharomyces cerevisiae alpha-factor,Rhizomucor miehei aspartic proteinase, and Myceliophthora thermophilalaccase (WO 95/33836).

Where both signal peptide and propeptide regions are present at theamino terminus of a polypeptide, the propeptide region is positionednext to the amino terminus of a polypeptide and the signal peptideregion is positioned next to the amino terminus of the propeptideregion.

It may also be desirable to add regulatory sequences which allow theregulation of the expression of the polypeptide relative to the growthof the host cell. Examples of regulatory systems are those which causethe expression of the gene to be turned on or off in response to achemical or physical stimulus, including the presence of a regulatorycompound. Regulatory systems in prokaryotic systems include the lac,lac, and trp operator systems. In yeast, the ADH2 system or GAL1 systemmay be used. In filamentous fungi, the TAKA alpha-amylase promoter,Aspergillus niger glucoamylase promoter, and Aspergillus oryzaeglucoamylase promoter may be used as regulatory sequences. Otherexamples of regulatory sequences are those which allow for geneamplification. In eukaryotic systems, these include the dihydrofolatereductase gene which is amplified in the presence of methotrexate, andthe metallothionein genes which are amplified with heavy metals. Inthese cases, the nucleotide sequence encoding the polypeptide would beoperably linked with the regulatory sequence.

Expression Vectors

The present invention also relates to recombinant expression vectorscomprising a polynucleotide of the present invention, a promoter, andtranscriptional and translational stop signals. The various nucleicacids and control sequences described herein may be joined together toproduce a recombinant expression vector which may include one or moreconvenient restriction sites to allow for insertion or substitution ofthe nucleotide sequence encoding the polypeptide at such sites.Alternatively, a polynucleotide sequence of the present invention may beexpressed by inserting the nucleotide sequence or a nucleic acidconstruct comprising the sequence into an appropriate vector forexpression. In creating the expression vector, the coding sequence islocated in the vector so that the coding sequence is operably linkedwith the appropriate control sequences for expression.

The recombinant expression vector may be any vector (e.g., a plasmid orvirus) which can be conveniently subjected to recombinant DNA proceduresand can bring about expression of the nucleotide sequence. The choice ofthe vector will typically depend on the compatibility of the vector withthe host cell into which the vector is to be introduced. The vectors maybe linear or closed circular plasmids.

The vector may be an autonomously replicating vector, i.e., a vectorwhich exists as an extrachromosomal entity, the replication of which isindependent of chromosomal replication, e.g., a plasmid, anextrachromosomal element, a minichromosome, or an artificial chromosome,The vector may contain any means for assuring self-replication.Alternatively, the vector may be one which, when introduced into thehost cell, is integrated into the genome and replicated together withthe chromosome(s) into which it has been integrated. Furthermore, asingle vector or plasmid or two or more vectors or plasmids whichtogether contain the total DNA to be introduced into the genome of thehost cell, or a transposon may be used.

The vectors of the present invention preferably contain one or moreselectable markers which permit easy selection of transformed,transfected, transduced, or the like cells. A selectable marker is agene the product of which provides for biocide or viral resistance,resistance to heavy metals, prototrophy to auxotrophs, and the like.

Examples of bacterial selectable markers are the dal genes from Bacillussubtilis or Bacillus licheniformis, or markers which confer antibioticresistance such as ampicillin, kanamycin, chloramphenicol, ortetracycline resistance. Suitable markers for yeast host cells are ADE2,HIS3, LEU2, LYS2, MET3, TRP1, and URA3. Selectable markers for use in afilamentous fungal host cell include, but are not limited to, amdS(acetamidase), argB (ornithine carbamoyltransferase), bar(phosphinothricin acetyltransferase), hph (hygromycinphosphotransferase), niaD (nitrate reductase), pyrG(orotidine-5′-phosphate decarboxylase), sC (sulfate adenyltransferase),and trpC (anthranilate synthase), as well as equivalents thereof.Preferred for use in an Aspergillus cell are the amdS and pyrG genes ofAspergillus nidulans or Aspergillus oryzae and the bar gene ofStreptomyces hygroscopicus.

The vectors of the present invention preferably contain an element(s)that permits integration of the vector into the host cell's genome orautonomous replication of the vector in the cell independent of thegenome.

For integration into the host cell genome, the vector may rely on thepolynucleotide's sequence encoding the polypeptide or any other elementof the vector for integration into the genome by homologous ornonhomologous recombination. Alternatively, the vector may containadditional nucleotide sequences for directing integration by homologousrecombination into the genome of the host cell at a precise location(s)in the chromosome(s). To increase the likelihood of integration at aprecise location, the integrational elements should preferably contain asufficient number of nucleic acids, such as 100 to 10,000 base pairs,preferably 400 to 10,000 base pairs, and most preferably 800 to 10,000base pairs, which have a high degree of identity with the correspondingtarget sequence to enhance the probability of homologous recombination.The integrational elements may be any sequence that is homologous withthe target sequence in the genome of the host cell. Furthermore, theintegrational elements may be non-encoding or encoding nucleotidesequences. On the other hand, the vector may be integrated into thegenome of the host cell by non-homologous recombination.

For autonomous replication, the vector may further comprise an origin ofreplication enabling the vector to replicate autonomously in the hostcell in question. The origin of replication may be any plasmidreplicator mediating autonomous replication which functions in a cell.The term “origin of replication” or “plasmid replicator” is definedherein as a nucleotide sequence that enables a plasmid or vector toreplicate in vivo.

Examples of bacterial origins of replication are the origins ofreplication of plasmids pBR322, pUC19, pACYC177, and pACYC184 permittingreplication in E. coli, and pUB110, pE194, pTA1060, and pAMβ1 permittingreplication in Bacillus.

Examples of origins of replication for use in a yeast host cell are the2 micron origin of replication, ARS1, ARS4, the combination of ARS1 andCEN3, and the combination of ARS4 and CEN6.

Examples of origins of replication useful in a filamentous fungal cellare AMA1 and ANS1 (Gems et al., 1991, Gene 98: 61-67; Cullen et al.,1987, Nucleic Acids Research 15: 9163-9175; WO 00/24883). Isolation ofthe AMA1 gene and construction of plasmids or vectors comprising thegene can be accomplished according to the methods disclosed in WO00/24883.

More than one copy of a polynucleotide of the present invention may beinserted into a host cell to increase production of the gene product. Anincrease in the copy number of the polynucleotide can be obtained byintegrating at least one additional copy of the sequence into the hostcell genome or by including an amplifiable selectable marker gene withthe polynucleotide where cells containing amplified copies of theselectable marker gene, and thereby additional copies of thepolynucleotide, can be selected for by cultivating the cells in thepresence of the appropriate selectable agent.

The procedures used to ligate the elements described above to constructthe recombinant expression vectors of the present invention are wellknown to one skilled in the art (see, e.g., Sambrook et al., 1989,supra).

Host Cells

The host cell may be any cell useful in the recombinant production of apolypeptide of the present invention, e.g., a prokaryote or a eukaryote.

The prokaryotic host cell may be any Gram positive bacterium or a Gramnegative bacterium. Gram positive bacteria include, but not limited to,Bacillus, Streptococcus, Streptomyces, Staphylococcus, Enterococcus,Lactobacillus, Lactococcus, Clostridium, Geobacillus, andOceanobacillus. Gram negative bacteria include, but not limited to, E.coli, Pseudomonas, Salmonella, Campylobacter, Helicobacter,Flavobacterium, Fusobacterium, Ilyobacter, Neisseria, and Ureaplasma.

The bacterial host cell may be any Bacillus cell. Bacillus cells usefulin the practice of the present invention include, but are not limitedto, Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis,Bacillus circulars, Bacillus clausii, Bacillus coagulans, Bacillusfirmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis,Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus,Bacillus subtilis, and Bacillus thuringiensis cells.

In a preferred aspect, the bacterial host cell is a Bacillusamyloliquefaciens, Bacillus lentus, Bacillus licheniformis, Bacillusstearothermophilus or Bacillus subtilis cell. In a more preferredaspect, the bacterial host cell is a Bacillus amyloliquefaciens cell. Inanother more preferred aspect, the bacterial host cell is a Bacillusclausii cell. In another more preferred aspect, the bacterial host cellis a Bacillus licheniformis cell. In another more preferred aspect, thebacterial host cell is a Bacillus subtilis cell.

The bacterial host cell may also be any Streptococcus cell.Streptococcus cells useful in the practice of the present inventioninclude, but are not limited to, Streptococcus equisimilis,Streptococcus pyogenes, Streptococcus uberis, and Streptococcus equisubsp. Zooepidemicus.

In a preferred aspect, the bacterial host cell is a Streptococcusequisimilis cell. In another preferred aspect, the bacterial host cellis a Streptococcus pyogenes cell. In another preferred aspect, thebacterial host cell is a Streptococcus uberis cell. In another preferredaspect, the bacterial host cell is a Streptococcus equi subsp.Zooepidemicus cell.

The bacterial host cell may also be any Streptomyces cell. Streptomycescells useful in the practice of the present invention include, but arenot limited to, Streptomyces achromogenes, Streptomyces avermitilis,Streptotnyces coelicolor, Streptomyces griseus, and Streptomyceslividans.

In a preferred aspect, the bacterial host cell is a Streptomycesachromogenes cell. In another preferred aspect, the bacterial host cellis a Streptomyces avermitilis cell. In another preferred aspect, thebacterial host cell is a Streptomyces coelicolor cell. In anotherpreferred aspect, the bacterial host cell is a Streptomyces griseuscell. In another preferred aspect, the bacterial host cell is aStreptomyces lividans cell.

The introduction of DNA into a Bacillus cell may, for instance, beeffected by protoplast transformation (see, e.g., Chang and Cohen, 1979,Molecular General Genetics 168: 111-115), by using competent cells (see,e.g., Young and Spizizen, 1961, Journal of Bacteriology 81: 823-829, orDubnau and Davidoff-Abelson, 1971, Journal of Molecular Biology 56:209-221), by electroporation (see, e.g., Shigekawa and Dower, 1988,Biotechniques 6: 742-751), or by conjugation (see, e.g., Koehier andThorne, 1987, Journal of Bacteriology 169: 5271-5278). The introductionof DNA into an E. coli cell may, for instance, be effected by protoplasttransformation (see, e.g., Hanahan, 1983, J. Mol. Biol. 166: 557-580) orelectroporation (see, e.g., Dower et al., 1988, Nucleic Acids Res. 16:6127-6145). The introduction of DNA into a Streptomyces cell may, forinstance, be effected by protoplast transformation and electroporation(see, e.g., Gong et al., 2004, Folia Microbiol. (Praha) 49: 399-405), byconjugation (see, e.g., Mazodier et al., 1989, J. Bacteriol. 171:3583-3585), or by transduction (see, e.g., Burke at al., 2001, Proc.Natl. Acad. Sci. USA 98:6289-6294). The introduction of DNA into aPseudomonas cell may, for instance, be effected by electroporation (see,e.g., Choi et al., 2006, J. Microbiol. Methods 64: 391-397) or byconjugation (see, e.g., Pinedo and Smets, 2005, Appl. Environ.Microbiol. 71: 51-57). The introduction of DNA into a Streptococcus cellmay, for instance, be effected by natural competence (see, e.g., Perryand Kuramitsu, 1981, Infect. Immun. 32: 1295-1297), by protoplasttransformation (see, e.g., Cott and Jollick, 1991, Microbios. 68:189-2070, by electroporation (see, e.g., Buckley et al. 1999, Appl.Environ. Microbiol. 65: 3800-3804) or by conjugation (see, e.g.,Clewell, 1981, Microbiol. Rev. 45: 409-436). However, any method knownin the for introducing DNA into a host cell can be used.

The host cell may also be a eukaryote, such as a mammalian, insect,plant, or fungal cell.

In a preferred aspect, the host cell is a fungal cell. “Fungi” as usedherein includes the phyla Ascomycota, Basidiomycota, Chytridiomycota,and Zygomycota (as defined by Hawksworth et al., In, Ainsworth andBisby's Dictionary of The Fungi, 8th edition, 1995, CAB International,University Press, Cambridge, UK) as well as the Oomycota (as cited inHawksworth et al., 1995, supra, page 171) and all mitosporic fungi(Hawksworth et al., 1995, supra).

In a more preferred aspect, the fungal host cell is a yeast cell.“Yeast” as used herein includes ascosporogenous yeast (Endomycetales),basidiosporogenous yeast, and yeast belonging to the Fungi Imperfecti(Blastomycetes). Since the classification of yeast may change in thefuture, for the purposes of this invention, yeast shall be defined asdescribed in Biology and Activities of Yeast (Skinner, F. A., Passmore,S. M., and Davenport, R. R., eds, Soc. App. Bacterial, Symposium SeriesNo. 9, 1980).

In an even more preferred aspect, the yeast host cell is a Candida,Hansenula, Kluyveromyces, Pichia, Saccharomyces, Schizosaccharomyces, orYarrowia cell.

In a most preferred aspect, the yeast host cell is a Saccharomycescarisbergensis, Saccharomyces cerevisiae, Saccharomyces diastaticus,Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomycesnorbensis, or Saccharomyces oviformis cell. In another most preferredaspect, the yeast host cell is a Kluyveromyces lactis cell. In anothermost preferred aspect, the yeast host cell is a Yarrowia lipolyticacell.

In another more preferred aspect, the fungal host cell is a filamentousfungal cell. “Filamentous fungi” include all filamentous forms of thesubdivision Eumycota and Oomycota (as defined by Hawksworth et al.,1995, supra). The filamentous fungi are generally characterized by amycelial wall composed of chitin, cellulose, glucan, chitosan, mannan,and other complex polysaccharides. Vegetative growth is by hyphalelongation and carbon catabolism is obligately aerobic. In contrast,vegetative growth by yeasts such as Saccharomyces cerevisiae is bybudding of a unicellular thallus and carbon catabolism may befermentative.

In an even more preferred aspect, the filamentous fungal host cell is anAcremonium, Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis,Chtysosporium, Coprinus, Conelus, Cryptococcus, Filibasidium, Fusarium,Humicola, Magnaperthe, Mucor, Myceliophthora, Neocallimastix,Neurospora, Paecilomyces, Penicillium, Phanerochaete, Phlebia,Piromyces, Pleurotus, Schizophyllum, Talaromyces, Thermoascus,Thielavia, Tolypocladium, Trametes, or Trichoderma cell.

In a most preferred aspect, the filamentous fungal host cell is anAspergillus awamori, Aspergillus fumigatus, Aspergillus foetidus,Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger orAspergillus oryzae cell. In another most preferred aspect, thefilamentous fungal host cell is a Fusarium bactridioides, Fusariumcerealis, Fusarium crookwellense, Fusarium culmorum, Fusariumgraminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi,Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusariumsambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusariumsuiphureum, Fusarium torulosum, Fusarium trichothecioides, or Fusariumvenenatum cell. In another most preferred aspect, the filamentous fungalhost cell is a Bjerkandera adusta, Ceriporiopsis aneirina, Ceriporiopsisaneirina, Ceriporiopsis caregiea, Ceriporiopsis gilvescens,Ceriporiopsis pannocinta, Ceriporiopsis rivulosa, Ceriporiopsis subrufa,Ceriporiopsis subvermispora, Chrysosporium keratinophilum, Chrysosporiumlucknowense, Chrysosporium tropicum, Chrysosporium merdarium,Chrysosporium inops, Chrysosporium pannicola, Chrysosporiumqueenslandicum, Chrysosporium zonatum, Coprinus cinereus, Coriolushirsutus, Humicola insolens, Humicola lanuginosa, Mucor miehei,Myceliophthora thermophila, Neurospora crassa, Penicillium brasilianum,Penicillium purpurogenum, Phanerochaete chrysosporium, Phlebia radiata,Pleurotus eryngii, Thielavia terrestris, Trametes villosa, Trametesversicolor, Trichoderma harzianum, Trichoderma koningii, Trichodermalongibrachiatum, Trichoderma reesei, or Trichoderma viride cell.

Fungal cells may be transformed by a process involving protoplastformation, transformation of the protoplasts, and regeneration of thecell wall in a manner known per se. Suitable procedures fortransformation of Aspergillus and Trichoderma host cells are describedin EP 238 023 and Yelton at al., 1984, Proceedings of the NationalAcademy of Sciences USA 81: 1470-1474. Suitable methods for transformingFusarium species are described by Malardier at al., 1989, Gene 78:147-156, and WO 96/00787. Yeast may be transformed using the proceduresdescribed by Becker and Guarente, in Abelson, J. N. and Simon, M. I.,editors, Guide to Yeast Genetics and Molecular Biology, Methods inEnzymology, Volume 194, pp 182-187, Academic Press, Inc., New York; Itoet al., 1983, Journal of Bacteriology 153: 163; and Hinnen et al., 1978,Proceedings of the National Academy of Sciences USA 75: 1920.

Methods of Production

The present invention also relates to methods for producing apolypeptide of the present invention, comprising: (a) cultivating acell, which in its wild-type form produces the polypeptide, underconditions conducive for production of the polypeptide; and (b)recovering the polypeptide. In a preferred aspect, the cell is of thegenus Thielavia. In a more preferred aspect, the cell is Thielaviaterrestris. In a most preferred aspect, the cell is Thielavia terrestrisNRRL 8126.

The present invention also relates to methods for producing apolypeptide of the present invention, comprising: (a) cultivating a hostcell under conditions conducive for production of the polypeptide; and(b) recovering the polypeptide.

The present invention also relates to methods for producing apolypeptide of the present invention, comprising: (a) cultivating a hostcell under conditions conducive for production of the polypeptide,wherein the host cell comprises a mutant nucleotide sequence having atleast one mutation in the mature polypeptide coding sequence of SEQ IDNO: 1 or SEQ ID NO: 3, wherein the mutant nucleotide sequence encodes apolypeptide which comprises or consists of the mature polypeptide of SEQID NO: 2 or SEQ ID NO: 4, and (b) recovering the polypeptide.

In a preferred aspect, the mature polypeptide is amino acids 19 to 396of SEQ ID NO: 2. In another preferred aspect, the mature polypeptide isamino acids 20 to 400 of SEQ ID NO: 4. In another preferred aspect, themature polypeptide coding sequence is nucleotides 110 to 1557 of SEQ IDNO: 1. In another preferred aspect, the mature polypeptide codingsequence is nucleotides 58 to 1200 of SEQ ID NO: 3.

In the production methods of the present invention, the cells arecultivated in a nutrient medium suitable for production of thepolypeptide using methods well known in the art. For example, the cellmay be cultivated by shake flask cultivation, and small-scale orlarge-scale fermentation (including continuous, batch, fed-batch, orsolid state fermentations) in laboratory or industrial fermentorsperformed in a suitable medium and under conditions allowing thepolypeptide to be expressed and/or isolated. The cultivation takes placein a suitable nutrient medium comprising carbon and nitrogen sources andinorganic salts, using procedures known in the art. Suitable media areavailable from commercial suppliers or may be prepared according topublished compositions (e.g., in catalogues of the American Type CultureCollection). If the polypeptide is secreted into the nutrient medium,the polypeptide can be recovered directly from the medium. If thepolypeptide is not secreted into the medium, it can be recovered fromcell lysates.

The polypeptides may be detected using methods known in the art that arespecific for the polypeptides. These detection methods may include useof specific antibodies, formation of an enzyme product, or disappearanceof an enzyme substrate. For example, an enzyme assay may be used todetermine the activity of the polypeptide as described herein.

The resulting polypeptide may be recovered using methods known in theart. For example, the polypeptide may be recovered from the nutrientmedium by conventional procedures including, but not limited to,centrifugation, filtration, extraction, spray-d ring, evaporation, orprecipitation.

The polypeptides of the present invention may be purified by a varietyof procedures known in the art including, but not limited to,chromatography (e.g., ion exchange, affinity, hydrophobic,chromatofocusing, and size exclusion), electrophoretic procedures (e.g.,preparative isoelectric focusing), differential solubility (e.g.,ammonium sulfate precipitation), SDS-PAGE, or extraction (see, e.g.,Protein Purification, J.-C. Janson and Lars Ryden, editors, VCHPublishers, New York, 1989) to obtain substantially pure polypeptides.

Plants

The present invention also relates to plants, e.g., a transgenic plant,plant part, or plant cell, comprising an isolated polynucleotideencoding a polypeptide having endoglucanase activity of the presentinvention so as to express and produce the polypeptide in recoverablequantities. The polypeptide may be recovered from the plant or plantpart. Alternatively, the plant or plant part containing the recombinantpolypeptide may be used as such for improving the quality of a food orfeed, e.g., improving nutritional value, palatability, and rheologicalproperties, or to destroy an antinutritive factor.

The transgenic plant can be dicotyledonous (a dicot) or monocotyledonous(a monocot). Examples of monocot plants are grasses, such as meadowgrass (blue grass, Poa), forage grass such as Festuca, Lolium, temperategrass, such as Agrostis, and cereals, e.g., wheat, oats, rye, barley,rice, sorghum, and maize (corn).

Examples of dicot plants are tobacco, legumes, such as lupins, potato,sugar beet, pea, bean and soybean, and cruciferous plants (familyBrassicaceae), such as cauliflower, rape seed, and the closely relatedmodel organism Arabidopsis thaliana.

Examples of plant parts are stem, callus, leaves, root, fruits, seeds,and tubers as well as the individual tissues comprising these parts,e.g., epidermis, mesophyll, parenchyme, vascular tissues, meristems.Specific plant cell compartments, such as chloroplasts, apoplasts,mitochondria, vacuoles, peroxisomes and cytoplasm are also considered tobe a plant part. Furthermore, any plant cell, whatever the tissueorigin, is considered to be a plant part. Likewise, plant parts such asspecific tissues and cells isolated to facilitate the utilisation of theinvention are also considered plant parts, e.g., embryos, endosperms,aleurone and seeds coats.

Also included within the scope of the present invention are the progenyof such plants, plant parts, and plant cells.

The transgenic plant or plant cell expressing a polypeptide of thepresent invention may be constructed in accordance with methods known inthe art. In short, the plant or plant cell is constructed byincorporating one or more expression constructs encoding a polypeptideof the present invention into the plant host genome or chloroplastgenome and propagating the resulting modified plant or plant cell into atransgenic plant or plant cell.

The expression construct is conveniently a nucleic acid construct whichcomprises a polynucleotide encoding a polypeptide of the presentinvention operably linked with appropriate regulatory sequences requiredfor expression of the nucleotide sequence in the plant or plant part ofchoice. Furthermore, the expression construct may comprise a selectablemarker useful for identifying host cells into which the expressionconstruct has been integrated and DNA sequences necessary forintroduction of the construct into the plant in question (the latterdepends on the DNA introduction method to be used).

The choice of regulatory sequences, such as promoter and terminatorsequences and optionally signal or transit sequences is determined, forexample, on the basis of when, where, and how the polypeptide is desiredto be expressed. For instance, the expression of the gene encoding apolypeptide of the present invention may be constitutive or inducible,or may be developmental, stage or tissue specific, and the gene productmay be targeted to a specific tissue or plant part such as seeds orleaves. Regulatory sequences are, for example, described by Tague atal., 1988, Plant Physiology 86: 506.

For constitutive expression, the 35S-CaMV, the maize ubiquitin 1, andthe rice actin 1 promoter may be used (Franck et al., 1980, Cell 21:285-294, Christensen et al., 1992, Plant Mo. Biol. 18: 675-689; Zhang etal., 1991, Plant Cell 3: 1155-1165). organ-specific promoters may be,for example, a promoter from storage sink tissues such as seeds, potatotubers, and fruits (Edwards & Coruzzi, 1990, Ann. Rev. Genet. 24;275-303), or from metabolic sink tissues such as meristems (Ito et al.,1994, Plant Mol. Biol. 24: 863-878), a seed specific promoter such asthe glutelin, prolamin, globulin, or albumin promoter from rice (Wu etal., 1998, Plant and Cell Physiology 39: 885-889), a Vicia faba promoterfrom the legumin B4 and the unknown seed protein gene from Vida faba(Conrad et al., 1998, Journal of Plant Physiology 152: 708-711), apromoter from a seed oil body protein (Chen et al., 1998, Plant and CellPhysiology 39: 935-941), the storage protein napA promoter from Brassicanapus, or any other seed specific promoter known in the art, e.g., asdescribed in WO 91/14772. Furthermore, the promoter may be a leafspecific promoter such as the rbcs promoter from rice or tomato (Kyozukaet al., 1993, Plant Physiology 102: 991-1000, the chlorella virusadenine methyltransferase gene promoter (Mitre and Higgins, 1994, PlantMolecular Biology 26: 85-93), or the aldP gene promoter from rice(Kagaya et al., 1995, Molecular and General Genetics 248: 668-674), or awound inducibie promoter such as the potato pint promoter (Xu et al.,1993, Plant Molecular Biology 22: 573-588). Likewise, the promoter mayinducible by abiotic treatments such as temperature, drought, oralterations in salinity or induced by exogenously applied substancesthat activate the promoter, e.g., ethanol, oestrogens, plant hormonessuch as ethylene, abscisic acid, and gibberellic add, and heavy metals.

A promoter enhancer element may also be used to achieve higherexpression of a polypeptide of the present invention in the plant. Forinstance, the promoter enhancer element may be an intron which is placedbetween the promoter and the nucleotide sequence encoding a polypeptideof the present invention. For instance, Xu et al., 1993, supra, disclosethe use of the first intron of the rice actin 1 gene to enhanceexpression.

The selectable marker gene and any other parts of the expressionconstruct may be chosen from those available in the art.

The nucleic acid construct is incorporated into the plant genomeaccording to conventional techniques known in the art, includingAgrobacterium-mediated transformation, virus-mediated transformation,microinjection, particle bombardment, biolistic transformation, andelectroporation (Gasser et al., 1990, Science 244: 1293; Potrykus, 1990,Bio/Technology 8: 535; Shimamoto et al., 1989, Nature 338: 274).

Presently, Agrobacterium tumefaciens-mediated gene transfer is themethod of choice for generating transgenic divots (for a review, seeHooykas and Schilperoort, 1992, Plant Molecular Biology 19: 15-38) andcan also be used for transforming monocots, although othertransformation methods are often used for these plants. Presently, themethod of choice for generating transgenic monocots is particlebombardment (microscopic gold or tungsten particles coated with thetransforming DNA) of embryonic calli or developing embryos (Christou,1992, Plant Journal 2: 275-281; Shimamoto, 1994, Current OpinionBiotechnology 5: 158-162; Vasil et al., 1992, Bio/Technology 10:667-674). An alternative method for transformation of monocots is basedon protoplast transformation as described by Omirulleh et al., 1993,Plant Molecular Biology 21: 415-428.

Following transformation, the transformants having incorporated theexpression construct are selected and regenerated into whole plantsaccording to methods well-known in the art. Often the transformationprocedure is designed for the selective elimination of selection geneseither during regeneration or in the following generations by using, forexample, co-transformation with two separate T-DNA constructs or sitespecific excision of the selection gene by a specific recombinase.

The present invention also relates to methods for producing apolypeptide of the present invention comprising: (a) cultivating atransgenic plant or a plant cell comprising a polynucleotide encoding apolypeptide having endoglucanase activity of the present invention underconditions conducive for production of the polypeptide; and (b)recovering the polypeptide.

Removal or Reduction of Endoglucanase Activity

The present invention also relates to methods for producing a mutant ofa parent cell, which comprises disrupting or deleting a polynucleotidesequence, or a portion thereof, encoding a polypeptide of the presentinvention, which results in the mutant cell producing less of thepolypeptide than the parent cell when cultivated under the sameconditions.

The mutant cell may be constructed by reducing or eliminating expressionof a nucleotide sequence encoding a polypeptide of the present inventionusing methods well known in the art, for example, insertions,disruptions, replacements, or deletions. In a preferred aspect, thenucleotide sequence is inactivated. The nucleotide sequence to bemodified or inactivated may be, for example, the coding region or a partthereof essential for activity, or a regulatory element required for theexpression of the coding region. An example of such a regulatory orcontrol sequence may be a promoter sequence or a functional partthereof, i.e., a part that is sufficient for affecting expression of thenucleotide sequence. Other control sequences for possible modificationinclude, but are not limited to, a leader, polyadenylation sequence,propeptide sequence, signal peptide sequence, transcription terminator,and transcriptional activator.

Modification or inactivation of the nucleotide sequence may be performedby subjecting the parent cell to mutagenesis and selecting for mutantcells in which expression of the nucleotide sequence has been reduced oreliminated. The mutagenesis, which may be specific or random, may beperformed, for example, by use of a suitable physical or chemicalmutagenizing agent, by use of a suitable oligonucleotide, or bysubjecting the DNA sequence to PCR generated mutagenesis. Furthermore,the mutagenesis may be performed by use of any combination of thesemutagenizing agents.

Examples of a physical or chemical mutagenizing agent suitable for thepresent purpose include ultraviolet (UV) irradiation, hydroxylamine,N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), O-methyl hydroxylamine,nitrous acid, ethyl methane sulphonate (EMS), sodium bisulphite, formicacid, and nucleotide analogues.

When such agents are used, the mutagenesis is typically performed byincubating the parent cell to be mutagenized in the presence of themutagenizing agent of choice under suitable conditions, and screeningand/or selecting for mutant cells exhibiting reduced or no expression ofthe gene.

Modification or inactivation of the nucleotide sequence may beaccomplished by introduction, substitution, or removal of one or morenucleotides in the gene or a regulatory element required for thetranscription or translation thereof. For example, nucleotides may beinserted or removed so as to result in the introduction of a stop codon,the removal of the start codon, or a change in the open reading frame.Such modification or inactivation may be accomplished by site-directedmutagenesis or PCR generated mutagenesis in accordance with methodsknown in the art. Although, in principle, the modification may beperformed in vivo, i.e., directly on the cell expressing the nucleotidesequence to be modified, it is preferred that the modification beperformed in vitro as exemplified below.

An example of a convenient way to eliminate or reduce expression of anucleotide sequence by a cell is based on techniques of genereplacement, gene deletion, or gene disruption. For example, in the genedisruption method, a nucleic acid sequence corresponding to theendogenous nucleotide sequence is mutagenized in vitro to produce adefective nucleic acid sequence which is then transformed into theparent cell to produce a defective gene. By homologous recombination,the defective nucleic acid sequence replaces the endogenous nucleotidesequence. It may be desirable that the defective nucleotide sequencealso encodes a marker that may be used for selection of transformants inwhich the nucleotide sequence has been modified or destroyed. In aparticularly preferred aspect, the nucleotide sequence is disrupted witha selectable marker such as those described herein.

Alternatively, modification or inactivation of the nucleotide sequencemay be performed by established anti-sense or RNAi techniques using asequence complementary to the nucleotide sequence. More specifically,expression of the nucleotide sequence by a cell may be reduced oreliminated by introducing a sequence complementary to the nucleotidesequence of the gene that may be transcribed in the cell and is capableof hybridizing to the mRNA produced in the cell. Under conditionsallowing the complementary anti-sense nucleotide sequence to hybridizeto the mRNA, the amount of protein translated is thus reduced oreliminated.

The present invention further relates to a mutant cell of a parent cellwhich comprises a disruption or deletion of a nucleotide sequenceencoding the polypeptide or a control sequence thereof, which results inthe mutant cell producing less of the polypeptide or no polypeptidecompared to the parent cell.

The polypeptide-deficient mutant cells so created are particularlyuseful as host cells for the expression of homologous and/orheterologous polypeptides. Therefore, the present invention furtherrelates to methods for producing a homologous or heterologouspolypeptide comprising: (a) cultivating the mutant cell under conditionsconducive for production of the) polypeptide; and (b) recovering thepolypeptide. The term “heterologous polypeptides” is defined herein aspolypeptides which are not native to the host cell, a native protein inwhich modifications have been made to alter the native sequence, or anative protein whose expression is quantitatively altered as a result ofa manipulation of the host cell by recombinant DNA techniques.

In a further aspect, the present invention relates to a method forproducing a protein product essentially free of endoglucanase activityby fermentation of a cell which produces both a polypeptide of thepresent invention as well as the protein product of interest by addingan effective amount of an agent capable of inhibiting endoglucanaseactivity to the fermentation broth before, during, or after thefermentation has been completed, recovering the product of interest fromthe fermentation broth, and optionally subjecting the recovered productto further purification.

In a further aspect, the present invention relates to a method forproducing a protein product essentially free of endoglucanase activityby cultivating the cell under conditions permitting the expression ofthe product, subjecting the resultant culture broth to a combined pH andtemperature treatment so as to reduce the endoglucanase activitysubstantially, and recovering the product from the culture broth.Alternatively, the combined pH and temperature treatment may beperformed on an enzyme preparation recovered from the culture broth. Thecombined pH and temperature treatment may optionally be used incombination with a treatment with an endoglucanase inhibitor.

In accordance with this aspect of the invention, it is possible toremove at least 60%, preferably at least 75%, more preferably at least85%, still more preferably at least 95%, and most preferably at least99% of the endoglucanase activity. Complete removal of endoglucanaseactivity may be obtained by use of this method.

The combined pH and temperature treatment is preferably carried out at apH in the range of 2-3 or 10-11 and a temperature in the range of atleast 75-85° C. for a sufficient period of time to attain the desiredeffect, where typically, 1 to 3 hours is sufficient.

The methods used for cultivation and purification of the product ofinterest may be performed by methods known in the art.

The methods of the present invention for producing an essentiallyendoglucanase-free product is of particular interest in the productionof eukaryotic polypeptides, in particular fungal proteins such asenzymes. The enzyme may be selected from, e.g., an amylolytic enzyme,lipolytic enzyme, proteolytic enzyme, cellulytic enzyme, oxidoreductase,or plant cell-wall degrading enzyme. Examples of such enzymes include anaminopeptidase, amylase, amyloglucosidase, carbohydrase,carboxypeptidase, catalase, cellulase, chitinase, cutinase, cyclodextringlycosyltransferase, deoxyribonuclease, esterase, galactosidase,beta-galactosidase, glucoamylase, glucose oxidase, glucosidase,haloperoxidase, hemicellulase, invertase, isomerase, laccase, ligase,lipase, lyase, mannosidase, oxidase, pectinolytic enzyme, peroxidase,phytase, phenoloxidase, polyphenoloxidase, proteolytic enzyme,ribonuclease, transferase, transglutaminase, or xylanase. Theendoglucanase-deficient cells may also be used to express heterologousproteins of pharmaceutical interest such as hormones, growth factors,receptors, and the like.

It will be understood that the term “eukaryotic polypeptides” includesnot only native polypeptides, but also those polypeptides, e.g.,enzymes, which have been modified by amino acid substitutions, deletionsor additions, or other such modifications to enhance activity,thermostability, pH tolerance and the like.

In a further aspect, the present invention relates to a protein productessentially free from endoglucanase activity which is produced by amethod of the present invention.

Methods of Inhibiting Expression of a Polypeptide

The present invention also relates to methods of inhibiting expressionof a polypeptide in a cell, comprising administering to the cell orexpressing in the cell a double-stranded RNA (dsRNA) molecule, whereinthe dsRNA comprises a subsequence or portion of a polynucleotide of thepresent invention. In a preferred aspect, the dsRNA is about 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25 or more duplex nucleotides in length. Inanother preferred aspect, the polypeptide has endoglucanase activity.

The dsRNA is preferably a small interfering RNA (siRNA) or a micro RNA(miRNA). In a preferred aspect, the dsRNA is small interfering RNA(siRNAs) for inhibiting transcription. In another preferred aspect, thedsRNA is micro RNA (miRNAs) for inhibiting translation.

The present invention also relates to such double-stranded RNA (dsRNA)molecules for inhibiting expression of a polypeptide in a cell, whereinthe dsRNA comprises a subsequence or portion of a polynucleotideencoding the mature polypeptide of SEQ ID NO: 2 or SEQ ID NO: 4. Whilethe present invention is not limited by any particular mechanism ofaction, the dsRNA can enter a cell and cause the degradation of asingle-stranded RNA (ssRNA) of similar or identical sequences, includingendogenous mRNAs. When a cell is exposed to dsRNA, mRNA from thehomologous gene is selectively degraded by a process called RNAinterference (RNAi).

The dsRNAs of the present invention can be used in gene-silencingtherapeutics. In one aspect, the invention provides methods toselectively degrade RNA using the dsRNAis of the present invention. Theprocess may be practiced in vitro, ex vivo or in vivo. In one aspect,the dsRNA molecules can be used to generate a loss-of-function mutationin a cell, an organ or an animal. Methods for making and using dsRNAmolecules to selectively degrade RNA are well known in the art, see, forexample, U.S. Pat. No. 6,506,559; U.S. Pat. No. 6,511,824; U.S. Pat. No.6,515,109; and U.S. Pat. No. 6,489,127.

Compositions

The present invention also relates to compositions comprising apolypeptide of the present invention. Preferably, the compositions areenriched in such a polypeptide. The term “enriched” indicates that theendoglucanase activity of the composition has been increased, e.g., withan enrichment factor of at least 1.1.

The composition may comprise a polypeptide of the present invention asthe major enzymatic component, e.g., a mono-component composition.Alternatively, the composition may comprise multiple enzymaticactivities, such as an aminopeptidase, amylase, carbohydrase,carboxypeptidase, catalase, cellulase, chitinase, cutinase, cyclodextringlycosyltransferase, deoxyribonuclease, esterase, alpha-galactosidase,beta-galactosidase, glucoamylase, alpha-glucosidase, beta-glucosidase,haloperoxidase, invertase, laccase, lipase, mannosidase, oxidase,pectinolytic enzyme, peptidoglutaminase, peroxidase, phytase,polyphenoloxidase, proteolytic enzyme, ribonuclease, transglutaminase,or xylanase. The additional enzyme(s) may be produced, for example, by amicroorganism belonging to the genus Aspergillus, preferably Aspergillusaculeatus, Aspergillus awamori, Aspergillus fumigatus, Aspergillusfoetidus Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger,or Aspergillus oryzae; Fusarium, preferably Fusarium bactridioides,Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusariumgraminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi,Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusariumsambucinum, Fusarium sarcochroum, Fusarium sulphureum, Fusariumtoruloseum, Fusarium trichothecioides, or Fusarium venenatum; Humicola,preferably Humicola insolens or Humicola lanuginosa; or Trichoderma,preferably Trichoderma harzianum, Trichoderma koningii, Trichodermalongibrachiatum, Trichoderma reesei, or Trichoderma viride.

The polypeptide compositions may be prepared in accordance with methodsknown in the art and may be in the form of a liquid or a drycomposition. For instance, the polypeptide composition may be in theform of a granulate or a microgranulate. The polypeptide to be includedin the composition may be stabilized in accordance with methods known inthe art.

Examples are given below of preferred uses of the polypeptidecompositions of the invention. The dosage of the polypeptide compositionof the invention and other conditions under which the composition isused may be determined on the basis of methods known in the art.

Uses

The present invention also relates to methods for degrading orconverting a cellulosic material, comprising: treating the cellulosicmaterial with a composition comprising an effective amount of apolypeptide having endoglucanase activity of the present invention. In apreferred aspect, the method further comprises recovering the degradedor converted cellulosic material.

The polypeptides and host cells of the present invention may be used inthe production of monosaccharides, disaccharides, and polysaccharides aschemical or fermentation feedstocks from cellulosic biomass for theproduction of ethanol, plastics, other products or intermediates. Thecomposition comprising the polypeptide having endoglucanase activity maybe in the form of a crude fermentation broth with or without the cellsremoved or in the form of a semi-purified or purified enzymepreparation. Alternatively, the composition may comprise a host cell ofthe present invention as a source of the polypeptide havingendoglucanase activity in a fermentation process with the biomass. Thehost cell may also contain native or heterologous genes that encodeother proteins and enzymes, mentioned above, useful in the processing ofbiomass. In particular, the polypeptides and host cells of the presentinvention may be used to increase the value of processing residues(dried distillers grain, spent grains from brewing, sugarcane bagasse,etc.) by partial or complete degradation of cellulose or hemicellulose.The compositions can also comprise other proteins and enzymes useful inthe processing of biomass, e.g., cellobiohydrolase, beta-glucosidase,hemicellulolytic enzymes, enhancers (WO 2005/074647, WO 2005/074656),etc.

In the methods of the present invention, any cellulosic material, suchas biomass, can be used. It is understood herein that the term“cellulosic material” encompasses lignocellulose. Biomass can include,but is not limited to, wood resources, municipal solid waste,wastepaper, crops, and crop residues (see, for example, Wiselogel etal., 1995, in Handbook on Bioethanol (Charles E. Wyman, editor), pp.105-118, Taylor & Francis, Washington D.C.; Wyman, 1994, BioresourceTechnology 50: 3-16; Lynd, 1990, Applied Biochemistry and Biotechnology24/25: 695-719; Mosier et al., 1999, Recent Progress in Bioconversion ofLignocellulosics, in Advances in Biochemical Engineering/Biotechnology,T, Scheper, managing editor, Volume 65, pp. 23-40, Springer-Verlag, NewYork).

The predominant polysaccharide in the primary cell wall of biomass iscellulose, the second most abundant is hemi-cellulose, and the third ispectin. The secondary cell wall, produced after the cell has stoppedgrowing, also contains polysaccharides and is strengthened by polymericlignin covalently cross-linked to hemicellulose. Cellulose is ahomopolymer of anhydrocellobiose and thus a linear beta-(1-4)-D-glucan,while hemicelluloses include a variety of compounds, such as xylans,xyloglucans, arabinoxylans, and mannans in complex branched structureswith a spectrum of substituents. Although generally polymorphous,cellulose is found in plant tissue primarily as an insoluble crystallinematrix of parallel glucan chains. Hemicelluloses usually hydrogen bondto cellulose, as well as to other hemiceliuloses, which help stabilizethe cell wall matrix.

Three major classes of enzymes are used to breakdown cellulosic biomass:

-   -   (1) The “endo-1,4-beta-glucanases” or        1,4-beta-D-glucan-4-glucanohydrolases (EC 3.2.1.4), which act        randomly on soluble and insoluble 1,4-beta-glucan substrates.    -   (2) The “exo-1,4-beta-D-glucanases” including both the        1,4-beta-D-glucan glucohydrolases (EC 3.2.1.74), which liberate        D-glucose from 1,4-beta-D-glucans and hydrolyze D-cellobiose        slowly, and cellobiohydrolases (1,4-beta-D-glucan        cellobiohydrolases, EC 3.2.1.91), which liberate D-cellobiose        from 1,4-beta-glucans.    -   (3) The “beta-D-glucosidases” or beta-D-glucoside        glucohydrolases (EC 32.1.21), which act to release D-glucose        units from cellobiose and soluble cellodextrins, as well as an        array of glycosides.

The polypeptides having endoglucanase activity of the present inventionare preferably used in conjunction with other cellulolytic proteins,e.g., exo-1,4-beta-D-glucanases and beta-D-glucosidases, to degrade thecellulose component of the biomass substrate, (see, for example, Brighamet al., 1995, in Handbook on Bioethanol (Charles E. Wyman, editor), pp.119-141, Taylor & Francis, Washington D.C.; Lee, 1997, Journal ofBiotechnology 56: 1-24). The term “cellulolytic proteins” is definedherein as those proteins or mixtures of proteins shown as being capableof hydrolyzing or converting or degrading cellulose under the conditionstested.

The exo-1,4-beta-D-glucanases and beta-D-glucosidases may be produced byany known method known in the art (see, e.g., Bennett, J. W. and LaSure,L. (eds.), More Gene Manipulations in Fungi, Academic Press, CA, 1991).

The optimum amounts of a polypeptide having endoglucanase activity andother cellulolytic proteins depends on several factors including, butnot limited to, the mixture of component cellulolytic proteins, thecellulosic substrate, the concentration of cellulosic substrate, thepretreatment(s) of the cellulosic substrate, temperature, time, pH, andinclusion of fermenting organism (e.g., yeast for SimultaneousSaccharification and Fermentation).

In a preferred aspect, the amount of polypeptide having endoglucanaseactivity per g of cellulosic material is about 0.5 to about 50 mg,preferably about 0.5 to about 40 mg, more preferably about 0.5 to about25 mg, more preferably about 0.75 to about 20 mg, more preferably about0.75 to about 15 mg, even more preferably about 0.5 to about 10 mg, andmost preferably about 2.5 to about 10 mg per g of cellulosic material.

In another preferred aspect, the amount of cellulolytic proteins per gof cellulosic material is about 0.5 to about 50 mg, preferably about 0.5to about 40 mg, more preferably about 0.5 to about 25 mg, morepreferably about 0.75 to about 20 mg, more preferably about 0.75 toabout 15 mg, even more preferably about 0.5 to about 10 mg, and mostpreferably about 2.5 to about 10 mg per g of cellulosic material.

In the methods of the present invention, the composition may besupplemented by one or more additional enzyme activities to improve thedegradation of the cellulosic material. Preferred additional enzymes arehemicellulases, esterases (e.g., lipases, phospholipases, and/orcutinases), proteases, laccases, peroxidases, or mixtures thereof.

In the methods of the present invention, the additional enzyme(s) may beadded prior to or during fermentation, including during or after thepropagation of the fermenting microorganism(s).

The enzymes may be derived or obtained from any suitable origin,including, bacterial, fungal, yeast or mammalian origin. The term“obtained” means herein that the enzyme may have been isolated from anorganism which naturally produces the enzyme as a native enzyme. Theterm “obtained” also means herein that the enzyme may have been producedrecombinantly in a host organism, wherein the recombinantly producedenzyme is either native or foreign to the host organism or has amodified amino acid sequence, e.g., having one or more amino acids whichare deleted, inserted and/or substituted, i.e., a recombinantly producedenzyme which is a mutant and/or a fragment of a native amino acidsequence or an enzyme produced by nucleic acid shuffling processes knownin the art. Encompassed within the meaning of a native enzyme arenatural variants and within the meaning of a foreign enzyme are variantsobtained recombinantly, such as by site-directed mutagenesis orshuffling.

The enzymes may also be purified. The term “purified” as used hereincovers enzymes free from other components from the organism from whichit is derived. The term “purified” also covers enzymes free fromcomponents from the native organism from which it is obtained. Theenzymes may be purified, with only minor amounts of other proteins beingpresent. The expression “other proteins” relate in particular to otherenzymes. The term “purified” as used herein also refers to removal ofother components, particularly other proteins and most particularlyother enzymes present in the cell of origin of the enzyme of theinvention. The enzyme may be “substantially pure,” that is, free fromother components from the organism in which it is produced, that is, forexample, a host organism for recombinantly produced enzymes. In apreferred aspect, the enzymes are at least 75% (w/w), preferably atleast 80%, more preferably at least 85%, more preferably at least 90%,more preferably at least 95%, more preferably at least 96%, morepreferably at least 97%, even more preferably at least 98%, or mostpreferably at least 99% pure. In another preferred aspect, the enzyme is100% pure.

The enzymes used in the present invention may be in any form suitablefor use in the processes described herein, such as, for example, a crudefermentation broth with or without cells, a dry powder or granulate, anon-dusting granulate, a liquid, a stabilized liquid, or a protectedenzyme. Granulates may be produced, e.g., as disclosed in U.S. Pat. Nos.4,106,991 and 4,661,452, and may optionally be coated by process knownin the art. Liquid enzyme preparations may, for instance, be stabilizedby adding stabilizers such as a sugar, a sugar alcohol or anotherpolyol, and/or lactic acid or another organic acid according toestablished process. Protected enzymes may be prepared according to theprocess disclosed in EP 238,216.

The methods of the present invention may be used to process a cellulosicmaterial to many useful organic products, chemicals and fuels. Inaddition to ethanol, some commodity and specialty chemicals that can beproduced from cellulose include xylose, acetone, acetate, glycine,lysine, organic acids (e.g., lactic acid), 1,3-propanediol, butanediol,glycerol, ethylene glycol, furfural, polyhydroxyalkanoates, ds,cis-muconic acid, and animal feed (Lynd, L. R., Wyman, C. E., andGerngross, T. U., 1999, Biocommodity Engineering, Biotechnol. Prog., 15:777-793; Philippidis, G. P., 1996, Cellulose bioconversion technology,in Handbook on Bloethanol: Production and Utilization, Wyman, C. E.,ed., Taylor & Francis, Washington, D.C., 179-212; and Ryu, D. D. Y., andMandels, M., 1980, Cellulases: biosynthesis and applications, Enz.Microb. Technol., 2: 91-102). Potential coproduction benefits extendbeyond the synthesis of multiple organic products from fermentablecarbohydrate. Lignin-rich residues remaining after biological processingcan be converted to lignin-derived chemicals, or used for powerproduction.

Conventional methods used to process the cellulosic material inaccordance with the methods of the present invention are well understoodto those skilled in the art. The methods of the present invention may beimplemented using any conventional biomass processing apparatusconfigured to operate in accordance with the invention.

Such an apparatus may include a batch-stirred reactor, a continuous flowstirred reactor with ultrafiltration, a continuous plug-flow columnreactor (Gusakov, A, V., and Sinitsyn, A. P., 1985, Kinetics of theenzymatic hydrolysis of cellulose: 1. A mathematical model for a batchreactor process, Enz. Microb. Technol. 7: 346-352), an attrition reactor(Ryu, S. K., and Lee, J. M., 1983, Bioconversion of waste cellulose byusing an attrition bioreactor, Biotechnol. Bioeng. 25: 53-65), or areactor with intensive stirring induced by an electromagnetic field(Gusakov, A. V., Sinitsyn, A. P., Davydkin, I. Y., Davydkin, V. Y.,Protas, O. V., 1996, Enhancement of enzymatic cellulose hydrolysis usinga novel type of bioreactor with intensive stirring induced byelectromagnetic field, Appl. Biochem. Biotechnol. 56: 141-153).

The conventional methods include, but are not limited to,saccharification, fermentation, separate hydrolysis and fermentation(SHF), simultaneous saccharification and fermentation (SSF),simultaneous saccharification and cofermentation (SSCF), hybridhydrolysis and fermentation (HHF), and direct microbial conversion(DMC).

SHF uses separate process steps to first enzymatically hydrolyzecellulose to glucose and then ferment glucose to ethanol. In SSF, theenzymatic hydrolysis of cellulose and the fermentation of glucose toethanol is combined in one step (Philippidis, G. P., 1996, Cellulosebioconversion technology, in Handbook on Bioethanol: Production andUtilization, Wyman, C. E., ed., Taylor & Francis, Washington, D.C.,179-212). SSCF includes the cofermentation of multiple sugars (Sheehan,J., and Himmel, M., 1999, Enzymes, energy and the environment: Astrategic perspective on the U.S. Department of Energy's research anddevelopment activities for bioethanol, Biotechnol. Prog. 15: 817-827).HHF includes two separate steps carried out in the same reactor but atdifferent temperatures, i.e., high temperature enzymaticsaccharification followed by SSF at a lower temperature that thefermentation strain can tolerate. DMC combines all three processes(cellulase production, cellulose hydrolysis, and fermentation) in onestep (Lynd, L. R., Weimer, P. J., van Zyl, W. H., and Pretorius, I. S.,2002, Microbial cellulose utilization: Fundamentals and biotechnology,Microbiol. Mol. Biol. Reviews 66: 596-577).

“Fermentation” or “fermentation process” refers to any fermentationprocess or any process comprising a fermentation step. A fermentationprocess includes, without limitation, fermentation processes used toproduce fermentation products including alcohols (e.g., arabinitol,butanol, ethanol, glycerol, methanol, 1,3-propanediol, sorbitol, andxylitol); organic acids (e.g., acetic acid, acetonic acid, adipic acid,ascorbic acid, citric acid, 2,5-diketo-D-&conic acid, formic acid,fumaric acid, glucaric acid, gluconic acid, glucuronic acid, glutaricacid, 3-hydroxypropionic acid, itaconic acid, lactic acid, malic acid,malonic acid, oxalic acid, propionic acid, succinic acid, and xylonicacid); ketones (e.g., acetone); amino acids (e.g., aspartic acid,glutamic acid, glycine, lysine, serine, and threonine); gases (e.g.,methane, hydrogen (H₂), carbon dioxide (CO₂), and carbon monoxide (CO)).Fermentation processes also include fermentation processes used in theconsumable alcohol industry (e.g., beer and wine), dairy industry (e.g.,fermented dairy products), leather industry, and tobacco industry.

The present invention further relates to methods of producing asubstance, comprising: (a) saccharifying a cellulosic material with acomposition comprising an effective amount of a polypeptide havingendoglucanase activity; (b) fermenting the saccharified cellulosicmaterial of step (a) with one or more fermentating microorganisms; and(c) recovering the substance from the fermentation. The compositioncomprising the polypeptide having endoglucanase activity may be in theform of a crude fermentation broth with or without the cells removed orin the form of a semi-purified or purified enzyme preparation or thecomposition may comprise a host cell of the present invention as asource of the polypeptide having endoglucanase activity in afermentation process with the biomass.

The substance can be any substance derived from the fermentation. In apreferred embodiment, the substance is an alcohol. It will be understoodthat the term “alcohol” encompasses a substance that contains one ormore hydroxyl moieties. In a more preferred embodiment, the alcohol isarabinitol. In another more preferred embodiment, the alcohol isbutanol. In another more preferred embodiment, the alcohol is ethanol.In another more preferred embodiment, the alcohol is glycerol. Inanother more preferred embodiment, the alcohol is methanol. In anothermore preferred embodiment, the alcohol is 1,3-propanediol. In anothermore preferred embodiment, the alcohol is sorbitol. In another morepreferred embodiment, the alcohol is xylitol. See, for example, Gong, C.S., Cao, N. J., Du, J., and Tsao, G. T., 1999, Ethanol production fromrenewable resources, in Advances in BiochemicalEngineering/Biotechnology, Scheper, T., ed., Springer-Verlag BerlinHeidelberg, Germany, 65; 207-241; Silveira, M. M., and Jonas, R., 2002,The biotechnological production of sorbitol, Appl. Microbiol.Biotechnol. 59: 400-408; Nigam, P., and Singh, D., 1995, Processes forfermentative production of xylitol—a sugar substitute, ProcessBiochemistry 30 (2); 117-124; Ezeji, T. C., Qureshi, N. and Blaschek,P., 2003, Production of acetone, butanol and ethanol by Clostridiumbeijerinckii BA101 and in situ recovery by gas stripping, World Journalof Microbiology and Biotechnology 19 (6): 595-603.

In another preferred embodiment, the substance is an organic acid. Inanother more preferred embodiment, the organic acid is acetic acid. Inanother more preferred embodiment, the organic acid is acetonic acid. Inanother more preferred embodiment, the organic acid is adipic acid. Inanother more preferred embodiment, the organic acid is ascorbic acid. Inanother more preferred embodiment, the organic acid is citric acid. Inanother more preferred embodiment, the organic acid is2,5-diketo-D-gluconic acid. In another more preferred embodiment, theorganic acid is formic acid. In another more preferred embodiment, theorganic acid is fumaric acid. In another more preferred embodiment, theorganic acid is glucaric acid. In another more preferred embodiment, theorganic acid is gluconic acid. In another more preferred embodiment, theorganic acid is glucuronic acid. In another more preferred embodiment,the organic acid is glutaric acid. In another preferred embodiment, theorganic acid is 3-hydroxypropionic acid. In another more preferredembodiment, the organic acid is itaconic acid. In another more preferredembodiment, the organic acid is lactic acid. In another more preferredembodiment, the organic acid is malic acid. In another more preferredembodiment, the organic acid is malonic acid. In another more preferredembodiment, the organic acid is oxalic acid. In another more preferredembodiment, the organic acid is propionic acid. In another morepreferred embodiment, the organic acid is succinic acid. In another morepreferred embodiment, the organic acid is xylonic acid. See, forexample, Chen, R., and Lee, Y. Y., 1997, Membrane-mediated extractivefermentation for lactic acid production from cellulosic biomass, Appl.Biochem. Biotechnol. 63-65: 435-448.

In another preferred embodiment, the substance is a ketone. It will beunderstood that the term “ketone” encompasses a substance that containsone or more ketone moieties. In another more preferred embodiment, theketone is acetone. See, for example, Qureshi and Blaschek, 2003, supra.

In another preferred embodiment, the substance is an amino acid. Inanother more preferred embodiment, the organic acid is aspartic acid. Inanother more preferred embodiment, the amino acid is glutamic acid. Inanother more preferred embodiment, the amino acid is glycine. In anothermore preferred embodiment, the amino acid is lysine. In another morepreferred embodiment, the amino acid is serine. In another morepreferred embodiment, the amino acid is threonine. See, for example,Richard, A., and Margaritis, A., 2004, Empirical modeling of batchfermentation kinetics for poly(glutamic acid) production and othermicrobial biopolymers, Biotechnology and Bioengineering 87 (4): 501-515.

In another preferred embodiment, the substance is a gas. In another morepreferred embodiment, the gas is methane. In another more preferredembodiment, the gas is H₂. In another more preferred embodiment, the gasis CO₂. In another more preferred embodiment, the gas is CO. See, forexample, Kataoka, N., A. Miya, and K. Kiriyama, 1997, Studies onhydrogen production by continuous culture system of hydrogen-producinganaerobic bacteria, Water Science and Technology 36 (6-7): 41-47; andGunaseelan V. N. in Biomass and Bioenergy, Vol. 13 (1-2), pp. 83-114,1997, Anaerobic digestion of biomass for methane production: A review.

Production of a substance from cellulosic material typically requiresfour major steps. These four steps are pretreatment, enzymatichydrolysis, fermentation, and recovery. Exemplified below is a processfor producing ethanol, but it will be understood that similar processescan be used to produce other substances, for example, the substancesdescribed above.

Pretreatment. In the pretreatment or pre-hydrolysis step, the cellulosicmaterial is heated to break down the lignin and carbohydrate structure,solubilize most of the hemicellulose, and make the cellulose fractionaccessible to cellulolytic enzymes. The heating is performed eitherdirectly with steam or in slurry where a catalyst may also be added tothe material to speed up the reactions. Catalysts include strong acids,such as sulfuric acid and SO₂, or alkali, such as sodium hydroxide. Thepurpose of the pre-treatment stage is to facilitate the penetration ofthe enzymes and microorganisms. Cellulosic biomass may also be subjectto a hydrothermal steam explosion pre-treatment (See U.S. PatentApplication No. 20020164730).

Saccharification. In the enzymatic hydrolysis step, also known assaccharification, enzymes as described herein are added to thepretreated material to convert the cellulose fraction to glucose and/orother sugars. The saccharification is generally performed instirred-tank reactors or fermentors under controlled pH, temperature,and mixing conditions. A saccharification step may last up to 200 hours.Saccharification may be carried out at temperatures from about 30° C. toabout 65° C., in particular around 50° C., and at a pH in the rangebetween about 4 and about 5, especially around pH 4.5. To produceglucose that can be metabolized by yeast, the hydrolysis is typicallyperformed in the presence of a beta-glucosidase.

Fermentation. In the fermentation step, sugars, released from thecellulosic material as a result of the pretreatment and enzymatichydrolysis steps, are fermented to ethanol by a fermenting organism,such as yeast. The fermentation can also be carried out simultaneouslywith the enzymatic hydrolysis in the same vessel, again under controlledpH, temperature, and mixing conditions. When saccharification andfermentation are performed simultaneously in the same vessel, theprocess is generally termed simultaneous saccharification andfermentation or SSF.

Any suitable cellulosic substrate or raw material may be used in afermentation process of the present invention. The substrate isgenerally selected based on the desired fermentation product, i.e., thesubstance to be obtained from the fermentation, and the processemployed, as is well known in the art. Examples of substrates suitablefor use in the methods of present invention include cellulose-containingmaterials, such as wood or plant residues or low molecular sugars DP1-3obtained from processed cellulosic material that can be metabolized bythe fermenting microorganism, and which may be supplied by directaddition to the fermentation medium.

The term “fermentation medium” will be understood to refer to a mediumbefore the fermenting microorganism(s) is(are) added, such as, a mediumresulting from a saccharification process, as well as a medium used in asimultaneous saccharification and fermentation process (SSF).

“Fermenting microorganism” refers to any microorganism suitable for usein a desired fermentation process. Suitable fermenting microorganismsaccording to the invention are able to ferment, i.e., convert, sugars,such as glucose, xylose, arabinose, mannose, galactose, oroligosaccharides directly or indirectly into the desired fermentationproduct. Examples of fermenting microorganisms include fungal organisms,such as yeast. Preferred yeast includes strains of the Saccharomycesspp., and in particular, Saccharomyces cerevisiae. Commerciallyavailable yeast include, e.g., Red Star®/™/Lesaffre Ethanol Red(available from Red Startesaffre, USA) FALI (available fromFleischmann's Yeast, a division of Burns Philp Food Inc., USA),SUPERSTART (available from Alltech), GERT STRAND (available from GertStrand AB, Sweden) and FERMIOL (available from DSM Specialties).

In a preferred embodiment, the yeast is a Saccharomyces spp. In a morepreferred embodiment, the yeast is Saccharomyces cerevisiae. In anothermore preferred embodiment, the yeast is Saccharomyces distaticus. Inanother more preferred embodiment, the yeast is Saccharomyces uvarum. Inanother preferred embodiment, the yeast is a Kluyveromyces. In anothermore preferred embodiment, the yeast is Kluyveromyces marxianus. Inanother more preferred embodiment, the yeast is Kluyveromyces fragilis.In another preferred embodiment, the yeast is a Candida. In another morepreferred embodiment, the yeast is Candida pseudotropicalis. In anothermore preferred embodiment, the yeast is Candida brassicae. In anotherpreferred embodiment, the yeast is a Clavispora. In another morepreferred embodiment, the yeast is Clavispora lusitaniae. In anothermore preferred embodiment, the yeast is Clavispora opuntiae. In anotherpreferred embodiment, the yeast is a Pachysolen. In another morepreferred embodiment, the yeast is Pachysolen tannophilus. In anotherpreferred embodiment, the yeast is a Bretannomyces. In another morepreferred embodiment, the yeast is Bretannomyces clausenii (Philippidis,G. P., 1996, Cellulose bioconversion technology, in Handbook onBioethanol: Production and Utilization, Wyman, C. E., ed., Taylor &Francis, Washington, D.C., 179-212).

Bacteria that can efficiently ferment glucose to ethanol include, forexample, Zymomonas mobilis and Clostridium thermocellum (Philippidis,1996, supra).

It is well known in the art that the organisms described above can alsobe used to produce other substances, as described herein.

The cloning of heterologous genes in Saccharomyces cerevisiae (Chen, Z.,Ho, N. W. Y., 1993, Cloning and improving the expression of Pichiastipitis xylose reductase gene in Saccharomyces cerevisiae, App.Biochem. Biotechnol. 39-40: 135-147: Ho, N. W. Y., Chen, Z, Brainard, A.P., 1998, Genetically engineered Saccharomyces yeast capable ofeffectively cofermenting glucose and xylose, Appl. Environ. Microbiol,64: 1852-1859), or in bacteria such as Escherichia coli (Beall, D. S.,Ohta, K., Ingram, L. O., 1991, Parametric studies of ethanol productionfrom xylose and other sugars by recombinant Escherichia coli, Biotech.Bioeng. 38: 296-303), Kiebsiella oxytoca (Ingram, L. O., Gomes, P. F.,Lai, X., Moniruzzaman, M., Wood, B. E., Yomano, L. P., York, S. W.,1998, Metabolic engineering of bacteria for ethanol production,Biotechnol. Bioeng. 58: 204-214), and Zymomonas mobilis (Zhang, M.,Eddy, C., Deanda, K., Finkelstein, M., and Picataggio, S., 1995,Metabolic engineering of a pentose metabolism pathway in ethanologenicZymomonas mobilis, Science 267: 240-243; Deanda, K., Zhang, M., Eddy,C., and Picataggio, S., 1996, Development of an arabinose-fermentingZymomonas mobilis strain by metabolic pathway engineering, Appl.Environ. Microbiol. 62: 4465-4470) has led to the construction oforganisms capable of converting hexoses and pentoses to ethanol(cofermentation).

Yeast or another microorganism typically is added to the degradedcellulose or hydrolysate and the fermentation is ongoing for about 24 toabout 96 hours, such as about 35 to about 60 hours. The temperature istypically between about 26° C. to about 40° C., in particular at about32° C., and at about pH 3 to about pH 6, in particular around pH 4-5.

In a preferred embodiment, yeast or another microorganism is applied tothe degraded cellulose or hydrolysate and the fermentation is ongoingfor about 24 to about 96 hours, such as typically 35-60 hours. In apreferred embodiments, the temperature is generally between about 26 toabout 40° C., in particular about 32° C., and the pH is generally fromabout pH 3 to about pH 6, preferably around pH 4-5. Yeast or anothermicroorganism is preferably applied in amounts of approximately 10⁵ to10¹², preferably from approximately 10⁷ to 10¹⁰, especiallyapproximately 5×10⁷ viable count per ml of fermentation broth. During anethanol producing phase the yeast cell count should preferably be in therange from approximately 10⁷ to 10¹⁰, especially around approximately2×10⁸. Further guidance in respect of using yeast for fermentation canbe found in, e.g., “The Alcohol Textbook” (Editors K. Jacques, T. P.Lyons and D. R. Kelsall, Nottingham University Press, United Kingdom1999), which is hereby incorporated by reference.

The most widely used process in the art is the simultaneoussaccharification and fermentation (SSF) process where there is noholding stage for the saccharification, meaning that yeast and enzymeare added together.

For ethanol production, following the fermentation the mash is distilledto extract the ethanol. The ethanol obtained according to the process ofthe invention may be used as, e.g., fuel ethanol; drinking ethanol,i.e., potable neutral spirits, or industrial ethanol.

A fermentation stimulator may be used in combination with any of theenzymatic processes described herein to further improve the fermentationprocess, and in particular, the performance of the fermentingmicroorganism, such as, rate enhancement and ethanol yield. A“fermentation stimulator” refers to stimulators for growth of thefermenting microorganisms, in particular, yeast. Preferred fermentationstimulators for growth include vitamins and minerals. Examples ofvitamins include multivitamins, biotin, pantothenate, nicotinic acid,meso-inositol, thiamine, pyridoxine, para-aminobenzoic acid, folic acid,riboflavin, and Vitamins A, B, C, D, and E. See, e.g., Alfenore et al.,Improving ethanol production and viability of Saccharomyces cerevisiaeby a vitamin feeding strategy during fed-batch process, Springer-Verlag(2002), which is hereby incorporated by reference. Examples of mineralsinclude minerals and mineral salts that can supply nutrients comprisingP, K, Mg, S, Ca, Fe, Zn, Mn, and Cu.

Recovery. The alcohol is separated from the fermented cellulosicmaterial and purified by conventional methods of distillation. Ethanolwith a purity of up to about 96 vol. % ethanol can be obtained, whichcan be used as, for example, fuel ethanol, drinking ethanol, i.e.,potable neutral spirits, or industrial ethanol.

For other substances, any method known in the art can be used including,but not limited to, chromatography (e.g., on exchange, affinity,hydrophobic, chromatofocusing, and size exclusion), electrophoreticprocedures (e.g., preparative isoelectric focusing), differentialsolubility (e.g., ammonium sulfate precipitation), SDS-PAGE,distillation, or extraction.

In the methods of the present invention, the polypeptide havingendoglucanase activity and other cellulolytic protein(s) may besupplemented by one or more additional enzyme activities to improve thedegradation of the cellulosic material. Preferred additional enzymes arehemicellulases, esterases (e.g., lipases, phospholipases, and/orcutinases), proteases, laccases, peroxidases, or mixtures thereof.

In the methods of the present invention, the additional enzyme(s) may beadded prior to or during fermentation, including during or after thepropagation of the fermenting microorganism(s).

Signal Peptides

The present invention also relates to nucleic acid constructs comprisinga gene encoding a protein, wherein the gene is operably linked to anucleotide sequence encoding a signal peptide comprising or consistingof amino acids 1 to 18 of SEQ ID NO: 2 or amino acids 1 to 19 of SEQ IDNO: 4, wherein the gene is foreign to the first and second nucleotidesequences

In a preferred aspect, the nucleotide sequence comprises or consists ofnucleotides 56 to 109 of SEQ ID NO: 1. In another preferred aspect, thenucleotide sequence comprises or consists of nucleotides 1 to 57 of SEQID NO: 3.

The present invention also relates to recombinant expression vectors andrecombinant host cells comprising such nucleic acid constructs.

The present invention also relates to methods for producing a proteincomprising (a) cultivating such a recombinant host cell under conditionssuitable for production of the protein; and (b) recovering the protein.

The protein may be native or heterologous to a host cell. The term“protein” is not meant herein to refer to a specific length of theencoded product and, therefore, encompasses peptides, oligopeptides, andproteins. The term “protein” also encompasses two or more polypeptidescombined to form the encoded product. The proteins also include hybridpolypeptides which comprise a combination of partial or completepolypeptide sequences obtained from at least two different proteinswherein one or more may be heterologous or native to the host cell.Proteins further include naturally occurring allelic and engineeredvariations of the above mentioned proteins and hybrid proteins.

Preferably, the protein is a hormone or variant thereof, enzyme,receptor or portion thereof, antibody or portion thereof, or reporter.In a more preferred aspect, the protein is an oxidoreductase,transferase, hydrolase, lyase, isomerase, or ligase. In an even morepreferred aspect, the protein is an aminopeptidase, amylase,carbohydrase, carboxypeptidase, catalase, cellulase, chitinase,cutinase, cyclodextrin glycosyltransferase, deoxyribonuclease, esterase,alpha-galactosidase, beta-galactosidase, glucoamylase,alpha-glucosidase, beta-glucosidase, invertase, laccase, another lipase,mannosidase, mutanase, oxidase, pectinolytic enzyme, peroxidase,phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease,transglutaminase or xylanase.

The gene may be obtained from any prokaryotic, eukaryotic, or othersource.

The present invention is further described by the following exampleswhich should not be construed as limiting the scope of the invention.

EXAMPLES Materials

Chemicals used as buffers and substrates were commercial products of atleast reagent grade.

Strains

Thielavia terrestris NRRL 8126 was used as the source of the Family 6polypeptides having endoglucanase activity. Saccharomyces cerevisiaestrain W3124 (MATa; ura 3-52; leu 2-3, 112; his 3-D200; pep 4-1137;prc1::HIS3; prb1:: LEU2; cir⁺) was used for screening of Thielaviaterrestris NRRL 8126 expression libraries for endoglucanase activity.Aspergillus oryzae HowB104 strain (alpha-amylase negative) was used forexpression of the Thielavia terrestris NRRL 8126 CEL6B polypeptidehaving endoglucanase activity. Aspergillus oryzae JaL250 strain (WO99/61651) was used for expression of the Thielavia terrestris NRRL 8126CEL6C polypeptide having endoglucanase activity.

Media and Solutions

LB medium was composed per liter of 10 g of tryptone, 5 g of yeastextract, and 5 g of sodium chloride.

LB ampicillin medium was composed per liter of 10 g of tryptone, 5 g ofyeast extract, 5 g of sodium chloride, and 50 μg of ampicillin per ml(filter sterilized, added after autoclaving).

LB ampicillin plates were composed per liter of LB ampicillin medium and15 g of bacto agar.

YEG medium was composed of 0.5% yeast extract and 2% glucose.

YPD medium was composed of 1% yeast extract, 2% peptone, andfilter-sterilized 2% glucose added after autoclaving.

YPM medium was composed of 1% yeast extract, 2% peptone, andfilter-sterilized 2% maltodextrin added after autoclaving.

SC-URA medium with galactose was composed per liter of 100 ml of 10×Basal salts, 28 ml of 20% casamino acids without vitamins, 10 ml of 1%tryptophan, 3.6 ml of 5% threonine (filter sterilized, added afterautoclaving), and 100 ml of 20% galactose (filter sterilized, addedafter autoclaving).

SC-URA medium with glucose was composed per liter of 100 ml of 10× Basalsalts solution, 28 ml of 20% casamino acids without vitamins, 10 ml of1% tryptophan, 3.6 ml of 5% threonine (filter sterilized, added afterautoclaving), and 100 ml of 20% glucose (filter sterilized, added afterautoclaving).

10× Basal salts solution was composed per liter of 75 g of yeastnitrogen base, 113 g of succinic acid, and 68 g of NaOH.

SC-agar was composed per liter of SC-URA medium (with glucose orgalactose as indicated) and 20 g of agar.

0.1% AZCL HE cellulose SC agar plates with galactose were composed perliter of SC-URA medium with galactose, 20 g of agar, and 0.1% AZCL HEcellulose (Megazyme, Wicklow, Ireland).

PD medium with cellulose was composed per liter of 24 grams potatodextrose (Difco) and 30 grams of Solcafloc (Diacel available fromDicalie-Europe-Nord, Gent, Belgium)

Potato dextrose medium was composed per liter of 39 grams of potatodextrose (Difco).

PDA plates were composed per liter of 39 grams of potato dextrose agar.

MDU2BP medium was composed per liter of 45 g of maltose, 1 g ofMgSO₄.7H₂O, 1 g of NaCl, 2 g of K₂SO₄, 12 g of KH₂PO₄, 7 g of yeastextract, 2 g of urea, and 0.5 ml of AMG trace metals solution, pHadjusted to 5.0.

AMG trace metals solution was composed per liter of 14.3 g ofZnSO₄.7H₂O, 2.5 g of CuSO₄.5H₂O, 0.5 g of NiCl₂.6H₂O, 13.8 g ofFeSO₄.7H₂O, 8.5 g of MnSO₄.H₂O, and 3 g of citric acid.

COVE plates were composed per liter of 342.3 g of sucrose, 20 ml of COVEsalt solution, 10 ml of 1 M acetamide, 10 ml of 1.5 M CsCl₂, and 25 g ofNoble agar.

COVE salt solution was composed per liter of 26 g of KCl, 26 g ofMgSO₄.7H₂O, 76 g of KH₂PO₄, and 50 ml of COVE trace metals solution.

COVE trace metals solution was composed per liter of 0.04 g ofNa₂B₄O₇.10H₂O, 0.4 g of CuSO₄.5H₂O, 1.2 g of FeSO₄.7H₂O 0.7 g ofMnSO₄.H₂O, 0.8 g of Na₂MoO₂.H₂O and 10 g of ZnSO₄.7H₂O.

Trace metals solution was composed per liter of 41.2 mg of FeCl₃.6H₂O,11.6 mg of ZnSO₄.7H₂O, 5.4 mg of MnSO₄.H₂O, 2.0 mg of CuSO₄.5H₂O, 0.48mg of H₃BO₃, and 67.2 mg of citric acid.

SOC medium was composed of 2% tryptone, 0.5% yeast extract, 10 mM NaCl,2.5 mM KCl, 10 mM MgCl₂: 10 mM MgSO₄, and filter-sterilized glucose to20 mM, added after autoclaving.

Freezing medium was composed of 60% SOC medium and 40% glycerol.

2×YT medium was composed per liter of 16 g of tryptone, 10 g of yeastextract, 5 g of NaCl, and 15 g of Bacto agar.

TE was composed of 10 mM Tris pH 7.4 and 0.1 mM EDTA.

Example 1 Thielavia terrestris NRRL 8126 Genomic DNA Extraction

Thielavia terrestris NRRL 8126 was grown in 25 ml of YEG medium at 37°C. and 250 rpm for 24 hours. Mycelia were then collected by filtrationthrough Miracloth™ (CalBiochem, La Jolla, Calif., USA) and washed oncewith 25 ml of 10 mM Tris-1 mM EDTA (TE) buffer. Excess buffer wasdrained from the mycelia preparation, which was subsequently frozen inliquid nitrogen. The frozen mycelia preparation was ground to a finepowder in an electric coffee grinder, and the powder was added to adisposable plastic centrifuge tube containing 20 ml of TE buffer and 5ml of 20% w/v sodium dodecylsulfate (SDS). The mixture was gentlyinverted several times to ensure mixing, and extracted twice with anequal volume of phenol:chloroform:isoamyl alcohol (25:24:1 v/v/v).Sodium acetate (3 M solution) was added to the extracted sample to afinal concentration of 0.3 M followed by 2.5 volumes of ice cold ethanolto precipitate the DNA. The tube was centrifuged at 15,000×g for 30minutes to pellet the DNA. The DNA pellet was allowed to air-dry for 30minutes before resuspension in 0.5 ml of TE buffer. DNase-freeribonuclease A was added to the resuspended DNA pellet to aconcentration of 100 μg per ml and the mixture was then incubated at 37°C. for 30 minutes. Proteinase K (200 μg/ml) was added and the tube wasincubated an additional one hour at 37° C. Finally, the sample wascentrifuged for 15 minutes at 12,000×g, and the supernatant was appliedto a Qiaprep® 8 manifold (QIAGEN Inc., Valencia, Calif., USA). Thecolumns were washed twice with 1 ml of PB (QIAGEN Inc. Valencia, Calif.,USA) and 1 ml of PE (QIAGEN Inc., Valencia, Calif., USA) under vacuum.The isolated DNA was eluted with 100 μl of TE, precipitated withethanol, washed with 70% ethanol, dried under vacuum, resuspended in TEbuffer, and stored at 4° C.

To generate genomic DNA for PCR amplification, Thielavia terrestris NRRL8126 was grown in 50 ml of NNCYP medium supplemented with 1% glucose ina baffled shake flask at 42° C. and 200 rpm for 24 hours. Mycelia wereharvested by filtration, washed twice in TE (10 mM Tris-1 mM EDTA), andfrozen under liquid nitrogen. A pea-size, piece of frozen mycelia wassuspended in 0.7 ml of 1% lithium dodecyl sulfate in TE and disrupted byagitation with an equal volume of 0.1 mm zirconia/silica beads (BiospecProducts, Inc., Bartlesville, Okla., USA) for 45 seconds in a FastPrepFP120 (ThermoSavant, Holbrook, N.Y., USA). Debris was removed bycentrifugation at 13,000×g for 10 minutes and the cleared supernatantwas brought to 2.5 M ammonium acetate and incubated on ice for 20minutes. After the incubation period, the nucleic acids wereprecipitated by addition of 2 volumes of ethanol. After centrifugationfor 15 minutes in a microfuge at 4° C., the pellet was washed in 70%ethanol and air dried. The DNA was resuspended in 120 μl of 0.1×TE andincubated with 1 μl of DNase-free RNase A at 37° C. for 20 minutes.Ammonium acetate was added to 2.5 M and the DNA was precipitated with 2volumes of ethanol. The pellet was washed in 70% ethanol, air dried, andresuspended in TE buffer.

Example 2 PCR Amplification of a cel6b Gene Fragment from Thielaviaterrestris NRRL 8126 Genomic DNA

Primers were designed based upon conserved motifs found in other Family6 glycosyl hydrolases. The specific peptide sequences used for primerdesign were:

EPDSLANLVT (corresponding to amino acids 167 to 176 of SEQ ID NO: 2)W[I,V]KPGGE[C,S] (amino acids 343 to 350 of SEQ ID NO: 2)The CODEHOP strategy was employed (Rose at al., 1998, Nucleic Acids Res.26: 1628-1635′ to design the following primers:

Sense Primer: (SEQ ID NO: 5) 5′-AGCCCGACTCCCTGGCNAAYCTGGTNAC-3′Antisense Primer: (SEQ ID NO: 6) 5′-GCACTCGCCGCCNGGYTTNAYCCA-3′

PCR amplification was performed in a volume of 30 μl containing 1×AmpliTaq® buffer (Applied Biosystems, Foster City, Calif., USA), 2.5units of AmpliTaq'., DNA polymerase (Applied Biosystems, Foster City,Calif., USA), 1 μM of each sense and antisense primer, and approximately1 μg of genomic DNA from Thielavia terrestris. Amplification wasperformed in a Robocycler® (Stratagene, La Jolla, Calif., USA)programmed for 1 cycle at 96° C. for 3 minutes and 72° C. for 3 minutes(during which DNA polymerase was added); and 35 cycles each at 94° C.for 45 seconds, 58° C. for 45 seconds, and 72° C. for 1 minute; followedby a final extension at 72° C. for 7 minutes.

The reaction products were fractionated on a 1.6% agarose gel using 40mM Tris base-20 mM sodium acetate-1 mM disodium EDTA (TAE) buffer, and aband of approximately 800 bp was excised, purified using a QIAEX® II GelExtraction Kit (QIAGEN Inc., Valencia, Calif., USA), and subcloned usinga TOPO TA Kit (Invitrogen, Carlsbad, Calif., USA). The plasmid from oneE. coli transformant was sequenced and found to contain an insert of 789bp coding for a Family 6 protein (CEL6B). This plasmid was designatedpPH23 (FIG. 1).

Example 3 Thielavia terrestris NRRL 8126 Genomic DNA LibraryConstruction and Screening

A genomic DNA library of Thielavia terrestris NRRL 8126 was constructedusing the bacteriophage cloning vector λZipLox (Life Technologies,Gaithersburg, Md., USA) with E. coli Y1090ZL cells (Life Technologies,Gaithersburg, Md., USA) as a host for plating and purification ofrecombinant bacteriophage and E. coli DH10Bzip (Life Technologies,Gaithersburg, Md., USA) for excision of individual pZL1 clonescontaining the cel6b gene.

Thielavia terrestris NRRL 8126 genomic DNA prepared as described inExample 1 was partially digested with Tsp 5091 and size-fractionated on1% agarose gels using TAE buffer. DNA fragments migrating in the sizerange 3-7 kb were excised and eluted from the gel using Prep-a-Genereagents (BioRad Laboratories, Hercules, Calif., USA). The eluted DNAfragments were ligated with Eco RI-cleaved and dephosphorylated λZipLoxvector arms (Life Technologies, Gaithersburg, Md., USA), and theligation mixtures were packaged using commercial packaging extracts(Stratagene, La Jolla, Calif., USA). The packaged DNA libraries wereplated and amplified in E. coli Y1090ZL cells. The unamplifled genomicDNA library contained 3.1×10⁶ pfu/ml (background titers with no DNA were2.0×10⁴ pfu/ml.

A Thielavia terrestris cel6b probe fragment was amplified from pPH23using primers homologous to the TOPO vector and Herculase® DNAPolymerase (Stratagene, La Jolla, Calif., USA), as shown below.

(SEQ ID NO: 7) 5′-CTTGGTACCGAGCTCGGATCCACTA-3′ (SEQ ID NO: 8)5′-ATAGGGCGAATTGGGCCCTCTAGAT-3′

Fifty picomoles of each of the primers were used in a PCR reactioncontaining 10 ng of pPH23, 1× Herculase® Amplification Buffer(Stratagene, La Jolla, Calif., USA), 1 μl of 10 mM blend of dATP, dTTP,dGTP, and dCTP, and 2.5 units of Herculase® DNA Polymerase in a finalvolume of 50 μl. Amplification was performed in a Robocycler® programmedfor 1 cycle at 94° C. for 1 minute; and 20 cycles each at 94° C. for 30seconds, 55° C. for 30 seconds, and 72° C. for 1 minute. The heat blockthen went to a 4° C. soak cycle.

The reaction product was isolated on a 1.0% agarose gel using TAE bufferwhere a 0.8 kb product band was excised from the gel and purified usinga QIAquick® Gel Extraction Kit (QIAGEN Inc., Valencia, Calif., USA)according to the manufacturer's instructions. A twenty five ng sample ofthe fragment was radiolabeled with ³²P using a Prime-It® II Kit(Stratagene, La Jolla, Calif., USA).

Approximately 90,000 plaques from the library were screened byplaque-hybridization using the labeled PCR fragment as the probe. TheDNA was cross-linked onto membranes (Hybond N+, Amersham, ArlingtonHeights, Ill., USA) using a UV Stratalinkerr® (Stratagene, La Jolla,Calif., USA). The ³²P-radiolabeled gene fragment was denatured by addingsodium hydroxide to a final concentration of 0.1 M, and added to ahybridization solution containing 6×SSPE, 7% SDS at an activity ofapproximately 1×10⁶ cpm per ml of hybridization solution. The mixturewas incubated overnight at 65° C. in a shaking water bath. Followingincubation, the membranes were washed three times for fifteen minutes in0.2×SSC with 0.1% SDS at 65° C. The membranes were dried on blottingpaper for 15 minutes, wrapped in SaranWrap™, and exposed to X-ray filmovernight at 70° C. with intensifying screens (Kodak, Rochester, N.Y.,USA).

Based on the production of strong hybridization signals with the cel6bprobe described above, several plaques were chosen for further study.The plaques were purified twice in E. coli Y1090ZL cells and theinserted genes and pZL1 plasmid were subsequently excised from theλZipLox vector as pZL1-derivatives (D'Alessio et al., 1992, Focus®14:76) using in vivo excision by infection of E. coli DH10BZL cells(Life Technologies, Gaithersburg, Md., USA). The colonies wereinoculated into three ml of LB ampicillin medium and grown overnight at37° C. Miniprep DNA was prepared from each of these cultures using aBioRobot 9600 (QIAGEN Inc., Valencia, Calif., USA). A clone designatedpPH47 was shown by DNA sequencing to contain the full-length gene forcel6b.

The E. coli strain PaHa47 containing plasmid pPH47 was deposited withthe Agricultural Research Service Patent Culture Collection, NorthernRegional Research Center, 1815 University Street, Peoria, Ill., 61604,as NRRL B-30898, with a deposit date of Feb. 23, 2006.

Example 4 Characterization of the Thielavia terrestris NRRL 8126 GenomicSequence Encoding a CEL6B Endoglucanase

DNA sequencing of the Thielavia terrestris NRRL 8126 cel6b genomic clonewas performed with an Applied Biosystems Model 3700 Automated DNASequencer using version 3.1 Big-Dye™ terminator chemistry (AppliedBiosystems, Inc., Foster City, Calif., USA) and dGTP chemistry (AppliedBiosystems, Inc., Foster City, Calif., USA) and primer walking strategy.Nucleotide sequence data were scrutinized for quality and all sequenceswere compared to each other with assistance of PHRED/PHRAP software(University of Washington, Seattle, Wash., USA).

A gene model for the Thielavia terrestris cel6b genomic DNA sequence wasconstructed based on similarity to homologous endoglucanase genes fromFusarium oxysporum and Chrysosporium lucknowense (Accession numbersXP383804 and AAQ38151.1, respectively).

The nucleotide sequence (SEQ ID NO: 1) and deduced amino acid sequence(SEQ ID NO: 2) of the Thielavia terrestris cel6b gene are shown in FIG.2. The coding sequence is 1505 bp including the stop codon and isinterrupted by introns of 77, 127 and 110 bp. The encoded predictedprotein is 396 amino acids. The % G+C of the coding sequence of the gene(including introns) is 64.9% G+C and the mature polypeptide codingsequence is 64.6%. Using the SignalP program (Nielsen et al., 1997,Protein Engineering 10:1-6), a signal peptide of 18 residues waspredicted. The predicted mature protein contains 378 amino acids with amolecular mass of 40.6 kDa and an isoelectric pH of 5.01.

A comparative pairwise global alignment of amino acid sequences wasdetermined using the Needleman-Wunsch algorithm (Needleman and Wunsch,1970, J. Mol. Biol. 48: 443-453) as implemented in the Needle program ofEMBOSS with gap open penalty of 10, gap extension penalty of 0.5, andthe EBLOSUM62 matrix. The alignment showed that the deduced amino acidsequence of the Thielavia terrestris gene encoding the CEL6B polypeptidehaving endoglucanase activity shares 85% and 82% identity (excludinggaps) to the deduced amino acid sequences of two Family 6 glycosylhydrolase proteins from Chrysosporium lucknowense and Neurospora crassa,respectively (accession numbers AAQ38151 and Q7RXI7, respectively).

Example 5 Cloning and Expression of a Thielavia terrestris NRRL 8126cDNA Encoding a CEL6C Endoglucanase

Thielavia terrestris NRRL 8126 was cultivated in 200 ml of PD mediumwith cellulose at 30° C. for five days at 200 rpm. Mycelia from theshake flask culture were harvested by filtering the contents through afunnel lined with Miracloth™. The mycelia were then sandwiched betweentwo Miracloth™ pieces and blotted dry with absorbent paper towels. Themycelial mass was then transferred to Falcon® 1059 plastic centrifugetubes and frozen in liquid nitrogen. Frozen mycelia were stored in a−80° C. freezer until use.

The extraction of total RNA was performed with guanidinium thiocyanatefollowed by ultracentrifugation through a 5.7 M CsCl cushion, andisolation of poly(A)+RNA was carried out by oligo(dT)-cellulose affinitychromatography, using the procedures described in WO 94/14953.

Double-stranded cDNA was synthesized from 5 μg of poly(A)+RNA by theRNase H method (Gubler and Hoffman, 1983, Gene 25: 263-269, Sambrook etal., 1989, Molecular cloning: A laboratory manual, Cold Spring Harborlab., Cold Spring Harbor, N.Y., USA). The poly(A)⁺ RNA (5 μg in 5 μl ofDEPC (0.1% diethylpyrocarbonate)-treated water) was heated at 70° C. for8 minutes in a pre-siliconized, RNase-free Eppendorf® tube, quenched onice, and combined in a final volume of 50 μl with reverse transcriptasebuffer composed of 50 mM Tris-HCl, pH 8.3, 75 mM KCl, 3 mM MgCl₂, 10 mMdithiothreitol (DTT) (Bethesda Research Laboratories, Bethesda, Md.,USA), 1 mM of dATP, dGTP and dTTP, and 0.5 mM 5-methyl-dCTP (Pharmacia,Uppsala, Sweden), 40 units of human placental ribonuclease inhibitor(RNasin, Promega, Madison, Wis., USA), 1.45 μg of oligo(dT)₁₈-Not Iprimer (Pharmacia, Uppsala, Sweden), and 1000 units of SuperScript® IIRNase H reverse transcriptase (Bethesda Research Laboratories, Bethesda,Md., USA). First-strand cDNA was synthesized by incubating the reactionmixture at 45° C. for 1 hour. After synthesis, the mRNA:cDNA hybridmixture was gel filtrated through a MicroSpin S-400 HR spin column(Pharmacia, Uppsala, Sweden) according to the manufacturer'sinstructions.

After gel filtration, the hybrids were diluted in 250 μl of secondstrand buffer (20 mM Tris-HCl, pH 7.4, 90 mM KCl, 4.6 mM MgCl₂, 10 mM(NH₄) SO₄, 0.16 mM NAD) containing 200 μM of each dNTP, 60 units of E.coli DNA polymerase I (Pharmacia, Uppsala, Sweden), 5.25 units of RNaseH (Promega, Madison, Wis., USA), and 15 units of E. coli DNA ligase(Boehringer Mannheim, Manheim, Germany), Second strand cDNA synthesiswas performed by incubating the reaction tube at 16° C. for 2 hours andan additional 15 minutes at 25° C. The reaction was stopped by additionof EDTA to a final concentration of 20 mM followed by phenol andchloroform extractions.

The double-stranded cDNA was precipitated at −20° C. for 12 hours byaddition of 2 volumes of 96% ethanol and 0.2 volume of 10 M ammoniumacetate, recovered by centrifugation at 13,000×g, washed in 70% ethanol,dried, and resuspended in 30 μl of Mung bean nuclease buffer (30 mMsodium acetate pH 4.6, 300 mM NaCl, 1 mM ZnSO₄, 0.35 mM DTT, 2%glycerol) containing 25 units of Mung bean nuclease (Pharmacia, Uppsala,Sweden). The single-stranded hair-pin DNA was clipped by incubating thereaction at 30° C. for 30 minutes, followed by addition of 70 μl of 10mM Tris-HCl-1 mM EDTA pH 7.5, phenol extraction, and precipitation with2 volumes of 96% ethanol and 0.1 volume of 3 M sodium acetate pH 5.2 onice for 30 minutes.

The double-stranded cDNAs were recovered by centrifugation at 13,000×gand blunt-ended in 30 μl of T4 DNA polymerase buffer (20 mMTris-acetate, pH 7.9, 10 mM magnesium acetate, 50 mM potassium acetate,1 mM DTT) containing 0.5 mM of each dNTP and 5 units of T4 DNApolymerase (New England Biolabs, Ipswich, Mass., USA) by incubating thereaction mixture at 16° C. for 1 hour. The reaction was stopped byaddition of EDTA to a final concentration of 20 mM, followed by phenoland chloroform extractions, and precipitation for 12 hours at −20° C. byadding 2 volumes of 96% ethanol and 0.1 volume of 3 M sodium acetate pH5.2.

After the fill-in reaction the cDNAs were recovered by centrifugation at13,000×g, washed in 70% ethanol, and dried. The cDNA pellet wasresuspended in 25 μl of ligation buffer (30 mM Tris-HCl, pH 7.8, 10 mMMgCl₂, 10 mM DTT, 0.5 mM ATP) containing 2.5 μg of non-palindromic BstXI adaptors (Invitrogen, Carlsbad, Calif., USA), shown below, and 30units of T4 ligase (Promega, Madison, Wis., USA), and then incubated at16° C. for 12 hours. The reaction was stopped by heating at 65° C. for20 minutes and then cooled on ice for 5 minutes.

5-CTTTCCAGCACA-3′ (SEG ID NO: 9) 3′-GAAAGGTC-5′

The adapted cDNA was digested with Not I, followed by incubation for 2.5hours at 37° C. The reaction was stopped by heating at 65° C. for 10minutes. The cDNAs were size-fractionated by gel electrophoresis on a0.8% SeaPlaque® GTG low melting temperature agarose gel (CambrexCorporation, East Rutherford, N.J., USA) in 44 mM Tris Base, 44 mM boricacid, 0.5 mM EDTA (TBE) buffer to separate unligated adaptors and smallcDNAs. The cDNA was size-selected with a cut-off at 0.7 kb and rescuedfrom the gel by use of beta-agarase (New England Biolabs, Ipswich,Mass., USA) according to the manufacturer's instructions andprecipitated for 12 hours at −20° C. by adding two volumes of 96%ethanol and 0.1 volume of 3 M sodium acetate pH 5.2.

The directional, size-selected cDNA was recovered by centrifugation at13,000×g, washed in 70% ethanol, dried, and then resuspended in 30 μl of10 mM Tris-HCl-1 mM EDTA pH 7.5. The cDNAs were desalted by gelfiltration through a MicroSpin S-300 HR spin column according to themanufacturer's instructions. Three test ligations were carried out in 10μl of ligation buffer (30 mM Tris-HCl, pH 7.8, 10 mM MgCl₂, 10 mM DTT,0.5 mM ATP) containing 5 μl of double-stranded cDNA (reaction tubes #1and #2), 15 units of T4 ligase (Promega, Madison, Wis., USA), and 30 ng(tube #1), 40 ng (tube #2), and 40 ng (tube #3, the vector backgroundcontrol) of Bst XI-Not I cleaved pYES2.0 vector (invitrogen, Carlsbad,Calif., USA). The ligation reactions were performed by incubation at 16°C. for 12 hours, then heating at 70° C. for 20 minutes, and finallyadding 10 μl of water to each tube. One μl of each ligation mixture waselectroporated into 40 μl of electrocompetent E. coli DH10B cells(Bethesda Research Laboratories, Bethesda, Md., USA) as described bySambrook et al., 1989, supra.

The Thielavia terrestris NRRL 8126 cDNA library was established as poolsin E. coli DH10B. Each pool was made by spreading transformed E. coli onLB ampicillin plates, yielding 15,000-30,000 colonies/plate afterincubation at 37° C. for 24 hours. Twenty ml of LB ampicillin medium wasadded to the plate and the cells were suspended therein. The cellsuspension was shaken at 100 rpm in a 50 ml tube for 1 hour at 37° C.

The resulting Thielavia terrestris NRRL 8126 cDNA library consisted ofapproximately 10⁶ individual clones, with a vector background of 1%.Plasmid DNA from some of the library pools was isolated using a PlasmidMidi Kit (QIAGEN Inc., Valencia, Calif., USA) according to themanufacturer's instructions, and stored at −20° C.

One ml aliquots of purified plasmid DNA (100 ng/ml) from some of thelibrary pools (Example 1) were transformed into Saccharomyces cerevisiaeW3124 by electroporation (Becker and Guarante, 1991, Methods Enzymol,194: 182-187) and the transformants were plated on SC agar containing 2%glucose and incubated at 30° C. In total, 50-100 plates containing250-400 yeast colonies were obtained from each pool.

After 3-5 days of incubation, the SC agar plates were replica platedonto a set of 0.1% AZCL HE cellulose SC URA agar plates with galactose.The plates were incubated for 2-4 days at 30° C. and endoglucanasepositive colonies were identified as colonies surrounded by a blue halo.

Example 6 Characterization of the Thielavia terrestris NRRL 8126 cDNASequence Encoding a CEL6C Endoglucanase

Endoglucanase-expressing yeast colonies were inoculated into 20 ml ofYPD medium in 50 ml glass test tubes. The tubes were shaken at 200 rpmfor 2 days at 30° C. The cells were harvested by centrifugation for 10minutes at 3000 rpm in a Heraeus Megafuge 1.0R centrifuge with a75002252 rotor (Hanau, Germany).

DNA was isolated according to WO 94/14953 and dissolved in 50 μl ofdeionized water. The DNA was transformed into E. coli DH10B cells bystandard procedures according to Sambrook et al., 1989, supra. One E.coli transformant subsequently shown to contain the Thielavia terrestrisNRRL 8126 cel6c gene was designated pCIBG146 (FIG. 3) and used asmaterial for deposit of biological material, E. coli strain pCIBG146 wasdeposited as E. coli NRRL B-30901 on Feb. 23, 2006.

Plasmid DNA was isolated from the E. coli transformants using standardprocedures according to Sambrook et al., 1989, supra. The full lengthcDNA sequence of the cel6c gene from Thielavia terrestris NRRL 8126 wassequenced with a Taq DyeDeoxy Terminator Cycle Sequencing Kit (PerkinElmer, Wellesley, Mass., USA) and synthetic oligonucleotide primersusing an Applied Biosystems ABI PRISM™ 377 DNA Sequencer (ABI, FosterCity, Calif., USA) according to the manufacturer's instructions.

The nucleotide sequence (SEQ ID NO: 3) and deduced amino acid sequence(SEQ ID NO: 4) of the Thielavia terrestris cel6c gene are shown in FIG.4. The coding sequence is 1203 bp including the stop codon. The encodedpredicted protein is 400 amino acids. The % G+C of the coding sequenceof the gene is 60.0% and the mature polypeptide coding sequence is60.0%. Using the SignalP program (Nielsen et al., 1997, supra), a signalpeptide of 19 residues was predicted. The predicted mature proteincontains 381 amino acids with a molecular mass of 42.1 kDa and pl of6.76.

A comparative pairwise global alignment of amino acid sequences wasdetermined using the Needleman-Wunsch algorithm (Needleman and Wunsch,1970, supra) as implemented in the Needle program of EMBOSS with gapopen penalty of 10, gap extension penalty of 0.5, and the EBLOSUM62matrix. The alignment showed that the deduced amino acid sequence of theThielavia terrestris gene encoding the CEL6C polypeptide shares 50%, 49%and 48% identity (excluding gaps) to the deduced amino acid sequences ofthree Family 6 glycosyl hydrolase proteins from Neurospora crassa,Magnaporthe grisea, and Agaricus bisporus, respectively (accessionnumbers Q87B5, XP 368004, and P49075, respectively).

Example 7 Construction of pAlLo2 Expression Vector

Expression vector pAlLo1 was constructed by modifying pBANe6 (U.S. Pat.No. 6,461,837), which comprises a hybrid of the promoters from the genesfor Aspergillus niger neutral alpha-amylase and Aspergillus oryzaetriose phosphate isomerase (NA2-tpi promoter), Aspergillus nigeramyloglucosidase terminator sequence (AMG terminator), and Aspergillusnidulans acetamidase gene (amdS). All mutagenesis steps were verified bysequencing using Big-Dye™ terminator chemistry (Applied Biosystems,Inc., Foster City, Calif., USA). Modification of pBANe6 was performed byfirst eliminating three Nco I restriction sites at positions 2051, 2722,and 3397 bp from the amdS selection marker by site-directed mutagenesis.All changes were designed to be “silent” leaving the actual proteinsequence of the amdS gene product unchanged. Removal of these threesites was performed simultaneously with a GeneEditor™ in vitroSite-Directed Mutagenesis Kit (Promega, Madison, Wis., USA) according tothe manufacturer's instructions using the following primers (underlinednucleotide represents the changed base):

AMDS3NcoMut (2050): (SEQ ID NO: 10) 5′-GTGCCCCATGATACGCCTCCGG-3′AMDS2NcoMut (2721): (SEQ ID NO: 11) 5′-GAGTCGTATTTCCAAGGCTCCTGACC-3′AMDS1NcoMut (3396): (SEQ ID NO: 12) 5′-GGAGGCCATGAAGTGGACCAACGG-3′

A plasmid comprising all three expected sequence changes was thensubmitted to site-directed mutagenesis, using a QuickChangen®Site-Directed Mutagenesis Kit (Stratagene, La Jolla, Calif., USA), toeliminate the Nco I restriction site at the end of the AMG terminator atposition 1643. The following primers (underlined nucleotide representsthe changed base) were used for mutagenesis:

Upper Primer to mutagenize the AMG terminator sequence: (SEQ ID NO: 13)5′-CACCGTGAAAGCCATGCTCTTTCCTTCGTGTAGAAGACCAGACAG-3′Lower Primer to mutagenize the AMG terminator sequence: (SEQ ID NO: 14)5′-CTGGTCTTCTACACGAAGGAAAGAGCATGGCTTTCACGGTGTCTG-3′

The last step in the modification of pBANe6 was the addition of a newNco I restriction site at the beginning of the polylinker using aQuickChange™ Site-Directed Mutagenesis Kit and the following primers(underlined nucleotides represent the changed bases) to yield pAlLo1(FIG. 5).

Upper Primer to mutagenize the NA2-tpi promoter: (SEQ ID NO: 15)5′-CTATATACACAACTGGATTTACCATGGGCCCGCGGCCGCAGATC-3′Lower Primer to mutegenize the NA2-tpi promoter: (SEQ ID NO: 16)5′-GATCTGCGGCCGCGGGCCCATGGTAAATCCAGTTGTGTATATAG-3′

The amdS gene of pAlLo1 was swapped with the Aspergillus nidulans pyrGgene. Plasmid pBANe10 (FIG. 6) was used as a source for the pyrG gene asa selection marker, Analysis of the sequence of pBANe10 showed that thepyrG marker was contained within an Nsi I restriction fragment and doesnot contain either Nco I or Pac I restriction sites. Since the amdS isalso flanked by Nsi I restriction sites the strategy to switch theselection marker was a simple swap of Nsi I restriction fragments.Plasmid DNA from pAlLo1 and pBANe10 were digested with the restrictionenzyme Nsi I and the products purified by agarose gel electrophoresis.The Nsi I fragment from pBANe 10 containing the pyrG gene was ligated tothe backbone of pAlLo1 to replace the original Nsi I DNA fragmentcontaining the amdS gene, Recombinant clones were analyzed byrestriction enzyme digestion to determine that they had the correctinsert and also its orientation. A clone with the pyrG gene transcribedin the counterclockwise direction was selected. The new plasmid wasdesignated pAlLo2 (FIG. 7).

Example 8 Expression of Thielavia terrestris NRRL 8126 cel6bEndoglucanase Gene in Aspergillus oryzae

Two synthetic oligonucleotide primers, shown below, were designed to PCRamplify the full-length open reading frame from plasmid pPH47 encoding aCEL6B endoglucanase. An In-Fusion Cloning Kit (BD Biosciences, PaloAlto, Calif., USA) was used to clone the fragment directly into pAlLo2.

In-Fusion Forward primer: (SEQ ID NO: 17)5′-ACTGGATTACCATGAAGCTCTCGCAGTCG-3′ In-Fusion Reverse primer:(SEQ ID NO: 18) 5′-AGTCACCTCTAGTTAGAACGACGGCACGGC-3′Bold letters represent coding sequence. The remain ng sequence containssequence identity compared with the insertion sites of pAlLo2.

Fifty picomoles of each of the primers above were used in a PCR reactioncontaining 50 ng of pPH47 DNA, 1×Pfx Amplification Buffer (Invitrogen,Carlsbad, Calif., USA), 6 μl of 10 mM blend of dATP, dTTP, dGTP, anddCTP, 2.5 units of Platinum Pfx DNA Polymerase (Invitrogen, Carisbad,Calif.), 1 μl of 50 mM MgSO₄, and 5 μl of 10×pCRx Enhancer solution(Invitrogen, Carlsbad, Calif.) in a final volume of 50 μl. Theamplification was performed in an Eppendorf® Mastercycler® 5333(Eppendorf Scientific, Inc., Westbury, N.Y., USA) programmed for 1 cycleat 98° C. for 2 minutes; and 35 cycles each at 94° C. for 30 seconds,65° C. for 30 seconds, and 68′C for 1.5 minutes. After the 35 cycles,the reaction was incubated at 68° C. for 10 minutes and then cooled at10° C. until further processed. A 1.5 kb PCR reaction product wasisolated on a 0.8% GTG-agarose gel (Cambrex Bioproducts, EastRutherford, N.J., USA) using TAE buffer and 0.1 μg of ethidium bromideper ml. The DNA band was visualized with the aid of a Dark Reader™(Clare Chemical Research, Dolores, Colo., USA) to avoid UV-inducedmutations. The 1.5 kb DNA band was excised with a disposable razor bladeand purified using a QIAquick® Gel Extraction Kit (QIAGEN Inc.,Valencia, Calif., USA) according to the manufacturer's instructions.

The vector pAlLo2 was linearized by digestion with Nco I and Pac I(using conditions specified by the manufacturer). The fragment waspurified by gel electrophoresis and a QIAquick Gel Extraction Kit asdescribed above. Cloning of the purified PCR fragment into the purifiedlinearized pAlLo2 vector was performed with an In-Fusion Cloning Kit.The reaction (20 μl) contained 1× In-Fusion Buffer (BD Biosciences, PaloAlto, Calif., USA), 1×BSA (BD Biosciences, Palo Alto, Calif., USA), 1 μlof In-Fusion enzyme (diluted 1:10) (BD Biosciences, Palo Alto, Calif.,USA), 160 ng of pAlLo2 digested with Nco I and Pac I, and 50 ng of theThielavia terrestris cel6b purified PCR product. The reaction wasincubated at room temperature for 30 minutes. A 1 μl sample of thereaction were used to transform E. coli XL10 SoloPac® Gold cells(Stratagene, La Jolla, Calif.) according to the manufacturer'sinstructions. After the recovery period, two 100 μl aliquots from thetransformation reaction were plated onto 150 mm 2×YT plates supplementedwith 100 μg of ampicillin per ml. The plates were incubated overnight at37° C. A set of eight putative recombinant clones was selected at randomfrom the selection plates and plasmid DNA was prepared from each oneusing a BioRobot 9600. Clones were analyzed by Eco RI restrictiondigest. Two clones that had the expected restriction digest pattern werethen sequenced to confirm that there were no mutations in the clonedinsert. One of the clones had the correct sequence and was selected anddesignated pEJG105 (FIG. 8).

Aspergillus oryzae Jal250 (WO 99/61651) protoplasts were preparedaccording to the method of Christensen et al., 1988, Bio/Technology 6:1419-1422. Five micrograms of pEJG105 (as well as pAlLo2 as a vectorcontrol) were used to transform Aspergillus oryzae JAL250 protoplasts.

The transformation of Aspergillus oryzae Jal250 with pEJG105 yieldedabout 100 transformants. Five transformants were isolated to individualPDA plates and incubated for five days at 34° C.

Confluent spore plates were washed with 5 ml of 0.01% Tween 80 and thespore suspension was used to inoculate 25 ml of MDU2BP medium in 125 mlglass shake flasks. Transformant cultures were incubated at 34° C. withconstant shaking at 200 rpm. At day five post-inoculation, an aliquot ofeach culture was centrifuged at 12000×g. Five μl of each supernatantwere mixed with an equal volume of 2× loading buffer (10%beta-mercaptoethanol) and loaded onto a 1.5 mm 8%-16% Tris-GlycineSDS-PAGE gel and stained with SimplyBlue® SafeStain (Invitrogen,Carlsbad, Calif.). SDS-PAGE profiles of the culture broths showed thatfour out of five transformants had a new protein band of approximately40 kDa. Transformant number 1 was selected for further studies anddesignated Aspergillus oryzae EJG105.

Example 9 Expression of Thielavia terrestris NRRL 8126 cel6cEndoglucanase Gene in Aspergillus oryzae

The Thielavia terrestris NRRL 8126 cel6c gene was excised from thepYES2.0 vector using Bam HI and Xba I, and ligated into the Aspergillusexpression vector pHD414 (EP 238 023, WO 93/11249) using standardmethods (Sambrook et al., 1989, supra). The Aspergillus expressionvector pHD414 is a derivative of p775 (EP 238 023). The resultingplasmid was designated pA2BG146 (FIG. 9).

Protoplasts of Aspergillus oryzae HowB104 were prepared as described inWO 95/02043. One hundred microliters of protoplast suspension were mixedwith 5-25 μg of pA2BG146 in 10 μl of STC composed of 1.2 M sorbitol, 10mM Tris-HCl, pH 7.5, 10 mM CaCl₂) and further mixed with 5-25 μg ofp3SR2, an Aspergillus nidulans amdS gene carrying plasmid (Christensenat al., 1988, Bio/Technology 6: 1419-1422). The mixture was left at roomtemperature for 25 minutes. Two hundred microliters of 60% PEG 4000(BDH, Poole, England) (polyethylene glycol, molecular weight 4,000), 10mM CaCl₂, and 10 mM Tris-HCl pH 7.5 was added and gently mixed andfinally 0.85 ml of the same solution was added and gently mixed. Themixture was left at room temperature for 25 minutes, centrifuged at2,500×g for 15 minutes, and the pellet was resuspended in 2 ml of 1.2 Msorbitol. This sedimentation process was repeated, and the protoplastswere spread on COVE plates. After incubation for 4-7 days at 37° C.spores were picked and spread in order to isolate single colonies. Thisprocedure was repeated and spores of a single colony after the secondreisolation were stored.

Each of the transformants was inoculated in 10 ml of YPM medium. After2-5 days of incubation at 30° C., 200 rpm, the supernatant was removed.Endoglucanase activity was identified by applying 20 μl of culture brothto 4 mm diameter holes punched out in a 0.1% AZCL HE cellulose SC-agarplate and incubation overnight at 30° C. The presence of endoglucanaseactivity produced a blue halo around a colony. Several transformantbroths had endoglucanase activity that was significantly greater thanbroth from an untransformed Aspergillus oryzae background control, whichdemonstrated efficient expression of the CEL6C endoglucanase fromThielavia terrestris NRRL 8126 in Aspergillus oryzae.

Example 10 Large Shake Flask Cultures of Aspergillus oryzae Jal250Containing cel6b Gene

Aspergillus oryzae Jal250 containing pEJG105 spores were spread onto aPDA plate and incubated for five days at 34° C. The confluent sporeplate was washed twice with 5 ml of 0.01% Tween 80 to maximize thenumber of spores collected. The spore suspension was then used toinoculate 500 ml of MDU2BP medium in a two-liter Fernbach flask. Theculture was incubated at 34° C. with constant shaking (200 rpm). At dayfive post inoculum, the culture broth was collected by filtration on a500 milliliter, 75 mm Nylon filter unit with a pore size of 0.45 μm witha glass-fiber pre-filter (Nalgene Nunc International, Rochester, N.Y.,USA). A 5 μl sample of the broth was analyzed by SDS-PAGE as describedin Example 9 to confirm that the protein pattern was the same as the oneobtained before. The broth was shown to contain a 40 kDa protein band.

Example 11 Hydrolysis of Carboxymethylcellulose by Thielavia terrestrisCEL6B and Thielavia terrestris CEL6C Endoglucanases

Sodium salt of carboxymethylcellulose (CMC, type 7L2) with averagedegree of substitution (DS) of 0.7 was obtained from Aqualon Division ofHercules Inc. (Wilmington, Del., USA). A 6.25 mg per ml solution of CMCin 50 mM sodium acetate pH 5.0 was prepared by slowly adding CMC to avigorously agitated buffer, followed by heating to approximately 60° C.under continuous stirring until complete dissolution.

The Thielavia terrestris CEL6B and Thielavia terrestris CEL6Cendoglucanases (both expressed in Aspergillus oryzae Jal250 as describedin Examples 8 and 9, respectively) were concentrated anddesalted/exchanged to 50 mM sodium acetate pH 5.0 using a Centricon®Plus-20 centrifugal filter with a 5000 NMWL Biomax-5® membrane(Millipore, Bedford, Mass., USA). The concentrated and desalted enzymesolutions were stored at −20° C. The protein concentration in the enzymesolutions was determined by a BCA Microplate Assay using a BCA ProteinAssay Reagent Kit according to the manufacturer's instructions (PierceChemical Co., Rockford, Ill., USA).

Hydrolysis of CMC was carried out in Eppendorf® DeepWell Plates 96 (1.2ml, Eppendorf North America, Inc., Westbury, N.Y., USA) sealed by aALPS-300″; plate sealer (ABgene Inc., Rochester, N.Y., USA). Allreactions were run in 50 mM sodium acetate pH 5.0 in a 1 ml volumewithout stirring at 50° C. The initial substrate concentration was 5 mgper ml. Both enzymes were used at four different concentrations.Corresponding enzyme dilutions in 50 mM sodium acetate pH 5.0 wereprepared fresh before enzymatic hydrolysis from stock enzyme solutions.

After 70 hours of hydrolysis, 40 d aliquots were transferred from thehydrolysis reactions to a flat-bottomed 96-well microplate (CorningInc., Corning, N.Y., USA) and mixed with 160 μl of 128 mM Na₂CO₃-72.5 MNaHCO₃ to terminate the reactions. The diluted samples were analyzed forreducing sugars (RS) using a microplate p-hydroxybenzoic acid hydrazide(PHBAH) assay as described below.

A 90-μl aliquot of the diluted sample was placed into each well of a96-well conical-bottomed microplate (Corning Inc., Corning, N.Y., USA).The assay was initiated by adding 60 μl of 1.25% PHBAH in 2% sodiumhydroxide to each well. The uncovered plate was heated on a custom-madeheating block for 10 minutes at 95° C. After the microplate was cooledto room temperature, 35 μl of deionized water was added to each well. A100-μl aliquot was removed from each well and transferred to aflat-bottomed 96-well microplate (Corning Inc., Corning, N.Y., USA). Theabsorbance at 410 nm (A₄₁₀) was measured using a SpectraMAX® MicroplateReader (Molecular Devices, Sunnyvale, Calif., USA). The A₄₁₀ value wastranslated into glucose equivalents using a standard curve.

The standard curve was obtained using six glucose standards (0.005,0.010, 0.025, 0.050, 0.075, and 0.100 mg/ml), which were treatedsimilarly to the samples. Glucose standards were prepared by diluting 10mg/ml stock glucose solution with deionized water.

The degree of carboxymethylcellulose conversion to reducing sugars(hydrolysis yield, %) was calculated using the following equation:

RSYield_((%))=RS_((mg/ml))×100×162/(CMC_((mg/ml))×180)=RS_((mg/ml))×100/(CMC_((mg/ml))×1.111)

In this equation, RS is the concentration of reducing sugars in solutionmeasured in glucose equivalents (mg/ml), and the factor 1.111 reflectsthe weight gain in converting cellulose to glucose.

The assay results demonstrated that after 70 hours of hydrolysis theThielavia terrestris CEL6B and Thielavia terrestris CEL6C endoglucanaseswere able to hydrolyze from 2 to 4% of available glycosidic bonds incarboxymethylcellulose.

DEPOSIT OF BIOLOGICAL MATERIAL

The following biological material have been deposited under the terms ofthe Budapest Treaty with the Agricultural Research Service PatentCulture Collection, Northern Regional Research Center, 1815 UniversityStreet, Peoria, Ill., 61604, and given the following accession numbers:

Deposit Accession Number Date of Deposit E. coli PaHa47 (pPH47) NRRLB-30898 Feb. 23, 2006 E. coli (pCIBG146) NRRL B-30901 Feb. 23, 2006The strains have been deposited under conditions that assure that accessto the cultures will be available during the pendency of this patentapplication to one determined by the Commissioner of Patents andTrademarks to be entitled thereto under 37 C.F.R. §1.14 and 35 U.S.C.§122. The deposits represent substantially pure cultures of thedeposited strains. The deposits are available as required by foreignpatent laws in countries wherein counterparts of the subjectapplication, or its progeny are filed. However, it should be understoodthat the availability of a deposit does not constitute a license topractice the subject invention in derogation of patent rights granted bygovernmental action.

The invention described and claimed herein is not to be limited in scopeby the specific aspects herein disclosed, since these aspects areintended as illustrations of several aspects of the invention. Anyequivalent aspects are intended to be within the scope of thisinvention. Indeed, various modifications of the invention in addition tothose shown and described herein will become apparent to those skilledin the art from the foregoing description. Such modifications are alsointended to fall within the scope of the appended claims. In the case ofconflict, the present disclosure including definitions will control.

Various references are cited herein, the disclosures of which areincorporated by reference in their entireties.

1. An isolated polynucleotide encoding a polypeptide havingendoglucanase activity, selected from the group consisting of: (a) apolynucleotide encoding a polypeptide comprising an amino acid sequencehaving at least 90% identity with the mature polypeptide of SEQ ID NO: 2or the mature polypeptide of SEQ ID NO: 4; (b) a polynucleotide encodinga polypeptide which hybridizes under at least high stringency conditionswith (i) the mature polypeptide coding sequence of SEQ ID NO: 1 or themature polypeptide coding sequence of SEQ ID NO: 3, (ii) the cDNAsequence of the mature polypeptide coding sequence of SEQ ID NO: 1 orthe genomic DNA sequence of the mature polypeptide coding sequence ofSEQ ID NO: 3, or (iii) the full-length complementary strand of (i) or(ii), wherein high stringency conditions are defined as prehybridizationand hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 μg/ml sheared anddenatured salmon sperm DNA, and 50% formamide and washing three timeseach for 15 minutes using 2×SSC, 0.2% SDS at 65° C.; and (c) apolynucleotide encoding a polypeptide comprising a nucleotide sequencehaving at least 90% identity with the mature polypeptide coding sequenceof SEQ ID NO: 1 or the mature polypeptide coding sequence of SEQ ID NO:3.
 2. The polynucleotide of claim 1, wherein the polypeptide havingendoglucanase activity comprises an amino acid sequence having at least90% identity with the mature polypeptide of SEQ ID NO: 2 or the maturepolypeptide of SEQ ID NO:
 4. 3. The polynucleotide of claim 2, whereinthe polypeptide having endoglucanase activity comprises an amino acidsequence having at least 95% identity with the mature polypeptide of SEQID NO: 2 or the mature polypeptide of SEQ ID NO:
 4. 4. Thepolynucleotide of claim 3, wherein the polypeptide having endoglucanaseactivity comprises an amino acid sequence having at least 97% identitywith the mature polypeptide of SEQ ID NO: 2 or the mature polypeptide ofSEQ ID NO:
 4. 5. The polynucleotide of claim 1, which hybridizes underat least high stringency conditions with (i) the mature polypeptidecoding sequence of SEQ ID NO: 1 or the mature polypeptide codingsequence of SEQ ID NO: 3, (ii) the cDNA sequence of the maturepolypeptide coding sequence of SEQ ID NO: 1 or the genomic DNA sequenceof the mature polypeptide coding sequence of SEQ ID NO: 3, or (iii) thefull-length complementary strand of (i) or (ii), wherein high stringencyconditions are defined as prehybridization and hybridization at 42° C.in 5×SSPE, 0.3% SDS, 200 μg/ml sheared and denatured salmon sperm DNA,and 50% formamide and washing three times each for 15 minutes using2×SSC, 0.2% SDS at 65° C.
 6. The polynucleotide of claim 5, whichhybridizes under at least very high stringency conditions with (i) themature polypeptide coding sequence of SEQ ID NO: 1 or the maturepolypeptide coding sequence of SEQ ID NO: 3, (ii) the cDNA sequence ofthe mature polypeptide coding sequence of SEQ ID NO: 1 or the genomicDNA sequence of the mature polypeptide coding sequence of SEQ ID NO: 3,or (iii) the full-length complementary strand of (i) or (ii), whereinvery high stringency conditions are defined as prehybridization andhybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 μg/ml sheared anddenatured salmon sperm DNA, and 50% formamide and washing three timeseach for 15 minutes using 2×SSC, 0.2% SDS at 70° C.
 7. Thepolynucleotide of claim 1, which comprises a nucleotide sequence havingat least 90% identity with the mature polypeptide coding sequence of SEQID NO: 1 or the mature polypeptide of SEQ ID NO:
 3. 8. Thepolynucleotide of claim 7, which comprises a nucleotide sequence havingat least 95% identity with the mature polypeptide coding sequence of SEQID NO: 1 or the mature polypeptide of SEQ ID NO:
 3. 9. Thepolynucleotide of claim 8, which comprises a nucleotide sequence havingat least 97% identity with the mature polypeptide coding sequence of SEQID NO: 1 or the mature polypeptide of SEQ ID NO:
 3. 10. Thepolynucleotide of claim 1, which encodes a polypeptide havingendoglucanase activity comprising or consisting of the amino acidsequence of SEQ ID NO: 2 or SEQ ID NO:
 4. 11. The polynucleotide ofclaim 1, which encodes a polypeptide having endoglucanase activitycomprising or consisting of the mature polypeptide of SEQ ID NO: 2 orthe mature polypeptide of SEQ ID NO:
 4. 12. The polynucleotide of claim1, which is contained in plasmid pPH47 which is contained in E. coliNRRL B-30898 or plasmid pCIBG146 which is contained in E. coli NRRLB-30901.
 13. A nucleic acid construct comprising the polynucleotide ofclaim 1 operably linked to one or more control sequences that direct theproduction of the polypeptide in an expression host.
 14. A recombinantexpression vector comprising the nucleic acid construct of claim
 13. 15.A recombinant host cell comprising the nucleic acid construct of claim13.
 16. A method for producing a polypeptide having endoglucanaseactivity, comprising: (a) cultivating the recombinant host cell of claim15 under conditions conducive for production of the polypeptide; and (b)recovering the polypeptide.
 17. A method for producing a polypeptidehaving endoglucanase activity, comprising: (a) cultivating a transgenicplant or a plant cell comprising the polynucleotide of claim 1 underconditions conducive for production of the polypeptide; and (b)recovering the polypeptide.
 18. A transgenic plant, plant part or plantcell, which has been transformed with the polynucleotide of claim 1.